Lab Presentation

The work carried out in the Proteolysis Lab is centered on the analysis of the molecular determinants of function and regulation of proteolysis at the protein level. We study peptidases and their zymogens, mostly from host-microbiome interactions, as well as their complexes with small-molecule and protein inhibitors. Another line of research deals with the molecular analysis of other interaction mediators between animal hosts and their microbiomes. Employed techniques include molecular biology, biochemistry, biophysics, and X-ray crystallography, among others. Our lab is fully furnished with state-of-the-art equipment, which enables us to carry out cutting-edge science projects.

Macroglobulin like protease inhibitorRecently, among other projects, we unveiled the mechanism of action of a multidomain, 180 kDa, α2-macroglobulin (α2M)-like protease inhibitor encoded in the Escherichia coli genome, by applying biochemical and structural techniques. We found that the protein is a target for proteases of diverse catalytic mechanism and specificity, which cut in an unstructured bait region. This triggers a large conformational rearrangement in the molecule from a native to an induced form, which has been extensively studied. However, the inhibitor remains monomeric, contrarily to the tetrameric state of some mammalian α2Ms, and the entrapment of the protease is necessarily accomplished by covalent binding of a surface lysine of the protease through a conserved and highly reactive thioester bond. As a consequence, the protease becomes sterically hindered to reach globular substrates of high molecular weight, so its proteolytic activity is inhibited. Taking into account the periplasmatic localization of the inhibitor, we hypothesize that it is acting as an E. coli defense mechanism against invading proteases that may damage cell wall components.

Projects

  • Host-microbiome peptidases and other hydrolyses, their zimogens and inhibitory complexes. Read more
  • Non-hydrolytic host-microbiome interaction molecules. Read more
  • Other projects. Read more

Lab People

F. Xavier Gomis Ruth

F. Xavier Gomis Ruth

Research Professor CSIC

xgrcri@ibmb.csic.es
+34 934 020 186 / +34 934 020 187

Dr. Gomis-Rüth is the head of Proteolysis Laboratory at the Institute of Molecular Biology of Barcelona (IBMB) and is presently Director of the Structural Biology Unit.

Dr. Gomis-Rüth graduated in chemical engineering (1989) by the Institut Químic de Sarrià, Universitat Ramon Llull, of Barcelona. In 1989-1992, he worked in protein crystallography, mainly on proteolytic enzymes, under the supervision of W. Bode and R. Huber, Nobel Prize for Chemistry in 1988, at the Max-Planck Institute of Biochemistry (MPIB) in Martinsried (Germany). In 1992 he obtained a PhD from the Ludwig-Maximilian University of Munich (Germany), and, at the end of 1992, he moved to Barcelona to continue working in structural biochemistry and biophysics of proteases with F.X. Avilés at the Universitat Autònoma de Barcelona. During this time, he held EMBO and Marie Curie long-term fellowships. In 1995-1996, he worked again at the MPIB, and, in 1997, he joined the group of M. Coll of the Spanish Research Council (CSIC). He became tenured scientific collaborator of CSIC in 1999 and set up his own laboratory. In 2004, he became research scientist and in 2008 he became full professor.

A detailed CV can be obtained here.

Theodoros Goulas

Theodoros Goulas

Senior Research Associate

thgcri@ibmb.csic.es

Anna Cuppari

Anna Cuppari

Postdoctoral Researcher

acucri@ibmb.csic.es

Laura Mariño Puertas

Laura Mariño Puertas

PhD Student

lmpcri@ibmb.csic.es

Laura Del Amo Maestro

Laura del Amo Maestro

PhD Student

lamcri@ibmb.csic.es

Tibisay Guevara Puig

Tibisay Guevara Puig

Research Technician

tgpcri@ibmb.csic.es

Miguel Angel Blazquez Arias

Miguel Angel Blazquez Arias

Research Technician

mbacri@ibmb.csic.es

João Paulo Campos Fernandes

João Paulo Campos Fernandes

Visiting Scientist

jpcsetor@gmail.com

Soraia Dos Reis Mendes

Soraia dos Reis Mendes

PhD Student

Selected Publications


Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition.

I. Garcia-Ferrer, P. Arêde, J. Gómez-Blanco, D. Luque, S. Duquerroy, J.R. Castón, T. Goulas & F.X. Gomis-Rüth.

Proc. Natl. Acad. Sci. USA , 112, 8290-8295 (2015)

(highlighted by the Spanish Biophysical Society as one of four Papers of the Month by SBE Members in July; Biofísica Magazine, issue #2, May-August 2015, http://www.sbe.es/ph2015-07.asp; selected by the Spanish Society of Biochemistry and Molecular Biology as The Article of the Month, January 2016, http://www.sebbm.es/web/en/science-for-society/article-of-the-month).


LysargiNase mirrors trypsin for identification of protein C-termini and methylation sites.

P.F. Huesgen, P.F. Lange, L.D. Rogers, N. Solis, U. Eckhard, O. Kleifeld, T. Goulas, F.X. Gomis-Rüth & C.M. Overall

Nat. Meth., 2015. 12, 55-58. (2015)


Multiple stable conformations account for reversible concentration-depedent oligomerization and autoinhibition of a metamorphic metallopeptidase.

López-Pelegrín, M. Cerdà-Costa, A. Cintas-Pedrola, F. Herranz-Trillo, P. Bernadó, J.R. Peinado, J.L. Arolas & F.X. Gomis-Rüth.

Angew. Chem. Int. Ed., 53, 10624-10630 (2014)

(chosen for the frontispiece of the section on communications).


Structural basis for the sheddase function of human meprin β metalloproteinase at the plasma membrane.

J.L. Arolas, C. Broder, T. Jefferson, T. Guevara, E.E. Sterchi, W. Bode, W. Stöcker, C. Becker-Pauly & F.X. Gomis-Rüth.

Proc. Natl. Acad. Sci. USA, 109, 16131-16136. (2012)


The crystal structure of human α2-macroglobulin reveals a unique molecular cage.

Marrero, S. Duquerroy, S. Trapani, T. Goulas, T. Guevara, G.R. Andersen, J. Navaza, L. Sottrup-Jensen & F.X. Gomis-Rüth.

Angew. Chem. Int. Ed., 51, 3340-3344 (2012)

(chosen by the journal as a Very Important Paper and for the issue cover; comment in C. Meyer, W. Hinrichs & U. Hahn, Human α2-macroglobulin–another variation on the venus flytrap, Angew. Chem. Int. Ed., 51, 5045-5047).


Structural evidence for standard-mechanism inhibition in metallopeptidases from a complex poised to re-synthesize a peptide bond.

J.L. Arolas, T.O. Botelho, A. Vilcinskas & F.X. Gomis-Rüth. (2011)

Angew. Chem. Int. Ed., 50, 10357-10360.


Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog.

Goulas, J.L. Arolas & F.X. Gomis-Rüth

Proc. Natl. Acad. Sci. USA, 108, 1856-1861. (2011)


Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains.

D.R. Boer, J.A. Ruíz-Masó, J.R. López-Blanco, A.G. Blanco, M. Vives-Llàcer, P. Chacón, I. Usón, F. X. Gomis-Rüth, M. Espinosa, O. Llorca, G. del Solar & M. Coll

EMBO J., 28(11):1666-78 (2009)


Macrophage elastase (MMP-12) kills bacteria within murine macrophages.

A.M. Houghton, W.O. Hartzell, C.S. Robbins, F.X. Gomis-Rüth & S.D. Shapiro.

Nature, 460, 637-641. (2009)


Mammalian metallopeptidase inhibition at the defense barrier of Ascaris parasite.

L. Sanglas, F.X. Avilés, R. Huber, F.X. Gomis-Rüth & J.L. Arolas.

Proc. Natl. Acad. Sci. USA, 106, 1743-1747. (2009)


Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis.

H. Wójtowicz, T. Guevara, C. Tallant, M. Olczak, A. Sroka, J. Potempa, M. Solà, T. Olczak & F. X. Gomis-Rüth

PLoS Pathog., 5, e1000419. (2009)


Structure of activated thrombin-activatable fibrinolysis inhibitor, a molecular link between coagulation and fibrinolysis.

Sanglas, Z. Valnickova, J.L. Arolas, I. Pallarés, T. Guevara, M. Solà, T. Kristensen, J.J. Enghild, F.X. Avilés & F.X. Gomis-Rüth.

Mol. Cell, 31, 598-606. (2008)


Structure of human carboxypeptidase A4 with its endogenous protein inhibitor, latexin.

I. Pallarés, R. Bonet, R. García-Castellanos, S. Ventura, F.X. Avilés, J. Vendrell & F.X. Gomis-Rüth

Proc. Natl. Acad. Sci. USA, 102, 3978-3983. (2005)


Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC.

A. Guasch, M. Lucas, M. Cabezas, R. Pérez-Luque, F.X. Gomis-Rüth, F. de la Cruz & M. Coll

Nat. Struct. Biol., 10, 1002-1010. (2003)


The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase

F.X. Gomis-Rüth, G. Moncalián, R. Pérez-Luque, A. González, E. Cabezón, F. de la Cruz & M. Coll.

Nature, 409, 637-641. (2001)


Crystal structure of avian carboxypeptidase D domain II: a prototype for the regulatory metallocarboxypeptidase family.

F.X. Gomis-Rüth, V. Companys, Y. Qian, L.D. Fricker, J. Vendrell, F.X. Avilés & M. Coll

EMBO J., 18, 5817-5826. (1999)


Structure of proline iminopeptidase from Xanthomonas campestris pv. citri : a prototype for the prolyl oligopeptidase family.

F.J. Medrano, J. Alonso, J.L. García, A. Romero, W. Bode & F.X. Gomis-Rüth

EMBO J., 17, 1-9. (1998)


The structure of plasmid-encoded transcriptional repressor CopG, unliganded and bound to its operator.

F.X. Gomis-Rüth, M. Solà, P. Acebo, A. Párraga, A. Guasch, R. Eritja, A. González, M. Espinosa, G. del Solar & M. Coll

EMBO J., 17, 7404-7415. (1998)


Mechanism of inhibition of the human matrix metalloproteinase stromelysin-1 by TIMP-1.

F.X. Gomis-Rüth, K. Maskos, M. Betz, A. Bergner, R. Huber, K. Suzuki, N. Yoshida, H. Nagase, K. Brew, G.P. Bourenkov, H. Bartunik & W. Bode.

Nature, 389, 77-81. (1997)


The three-dimensional structure of the native ternary complex of bovine pancreatic procarboxypeptidase A with proproteinase E and chymotrypsinogen C.

F. X. Gomis-Rüth, M. Gómez, W. Bode, R. Huber & F. X. Avilés

EMBO J., 14, 4387-4394. (1995)


Structural interaction of natural and synthetic inhibitors with the venom metalloproteinase, atrolysin C (form d).

D. Zhang, I. Bothos, F.X. Gomis-Rüth, R. Doll, C. Blood, F.G. Njoroge, J.W. Fox, W. Bode & E.F. Meyer

Proc. Natl. Acad. Sci. USA, 91, 8447-8451.  (1994)


First structure of a snake venom metalloproteinase: a prototype for matrix metalloproteinases/collagenases.

F.X. Gomis-Rüth, L.F. Kress & W. Bode

EMBO J., 12, 4151-4157. (1993)


Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases.

W. Bode, F.X. Gomis-Rüth, R. Huber, R. Zwilling & W. Stöcker

Nature358, 164-167. (1992)


All Publications


Structural insights unravel the zymogenic mechanism of the virulence factor gingipain K from Porphyromonas gingivalis, a causative agent of gum disease from the human oral microbiome.

A. Pomowski, I. Usón, Z. Nowakowska, F. Veillard, M.N. Sztukowska, T. Guevara, T. Goulas, D. Mizgalska, M. Nowak, B. Potempa, J.A. Huntington, J. Potempa & & F.X. Gomis-Rüth.

J. Biol. Chem., 292, 5724-5735 (2017)

(highlighted in the March 2017 issue of the JBC Editorial Member Digest, “Bringing the gingipain”)


Structural and functional probing of PorZ, an essential bacterial surface component of the type-IX secretion system of human oral-microbiomic Porphyromonas gingivalis.

A.M. Lasica, T. Goulas, D. Mizgalska, X. Zhou, I. de Diego, M. Ksiazek, M. Madej, Y. Guo, T. Guevara, M. Nowak, B. Potempa, A. Goel, M. Sztukowska, A.T. Prabhakar, M. Bzowska, M. Widziolek, I.B. Thøgersen, J.J. Enghild, M. Simonian, A.W. Kulczyk, K.-A. Nguyen, J. Potempa & F.X. Gomis-Rüth

Sci. Rep., 6, 37708 (2016)

(highlighted by the Spanish Biophysical Society as one of Papers of the Month in November 2016 in Biofísica Magazine, issue #6, September-December 2016)


Structure of RagB, a major immunodominant outer-membrane surface receptor antigen of Porphyromonas gingivalis.

T. Goulas, I. Garcia-Ferrer, J.A. Hutcherson, B.A. Potempa, J. Potempa, D.A. Scott & F.X. Gomis-Rüth

Mol. Oral Microbiol., 31, 472-485. (2016)


The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal β-sandwich domain.

I. De Diego, M. Ksiazek, D. Mizgalska, L. Koneru, P. Golik, B. Szmigielski, M. Nowak, Z. Nowakowska, B. Potempa, J.A. Houston, J.J. Enghild, I.B. Thøgersen, J. Gao, A.H. Kwan, J. Trewhella, G. Dubin, F.X. Gomis-Rüth, K.-A. Nguyen & J. Potempa.

Sci. Rep., 6, 23123. (2016)


Enzymatic and structural characterization of the major endopeptidase in the Venus flytrap digestion fluid.

M.W. Risør, L.R. Thomsen, K.W. Sanggaard, T.A. Nielsen, I.B. Thøgersen, M.V. Lukassen, L. Rossen, I. Garcia-Ferrer, T. Guevara, C. Scavenius, E. Meinjohanns, F.X. Gomis-Rüth & J.J. Enghild

J. Biol. Chem., 291, 2271-2287 (2016)

(highlighted in the May 2016 issue of the magazine of the American Society for Biochemistry and Molecular Biology, ASBMB Today)


Structural basis for latency and function of immune inhibitor A metallopeptidase, a modulator of the Bacillus anthracis secretome.

J.L. Arolas, T. Goulas, A.P. Pomerantsev, S.H. Leppla & F.X. Gomis-Rüth.

Structure, 24, 25-36.  (2016)

(Preview in the same journal issue: Schacherl, M. & Baumann, U. (2016). Feeding anthrax: the crystal structure of Bacillus anthracis InhA protease. Structure, 24, 1-2).


Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition.

I. Garcia-Ferrer, P. Arêde, J. Gómez-Blanco, D. Luque, S. Duquerroy, J.R. Castón, T. Goulas & F.X. Gomis-Rüth.

Proc. Natl. Acad. Sci. USA , 112, 8290-8295 (2015)

(highlighted by the Spanish Biophysical Society as one of four Papers of the Month by SBE Members in July; Biofísica Magazine, issue #2, May-August 2015, http://www.sbe.es/ph2015-07.asp; selected by the Spanish Society of Biochemistry and Molecular Biology as The Article of the Month, January 2016, http://www.sebbm.es/web/en/science-for-society/article-of-the-month).


Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase.

T. Goulas, D. Mizgalska, I. Garcia-Ferrer, T. Kantyka, T. Guevara, B. Szmigielski, A. Sroka, C. Millán, I. Usón, F. Veillard, B. Potempa, P. Mydel, M. Solà, J. Potempa & F.X. Gomis-Rüth

Sci. Rep., 5, 11969 (2015)

(highlighted by the Spanish Biophysical Society as one of four Papers of the Month by SBE Members in July in Biofísica Magazine, issue #2, May-August 2015; http://www.sbe.es/ph2015-07.asp)


Structure of RagB, a major immunodominant outer-membrane surface receptor antigen of Porphyromonas gingivalis.

T. Goulas, I. Garcia-Ferrer, J.A. Hutcherson, B.A. Potempa, J. Potempa, D.A. Scott & F.X. Gomis-Rüth.

Mol. Oral Microbiol., doi: 10.1111/omi.12140. (2015)


LysargiNase mirrors trypsin for identification of protein C-termini and methylation sites.

P.F. Huesgen, P.F. Lange, L.D. Rogers, N. Solis, U. Eckhard, O. Kleifeld, T. Goulas, F.X. Gomis-Rüth & C.M. Overall

Nat. Meth., 2015. 12, 55-58. (2015)


A novel mechanism of latency in matrix metalloproteinases.

M. López-Pelegrín, M. Ksiazek, A.Y. Karim, T. Guevara, Joan L. Arolas, J. Potempa & F.X. Gomis-Rüth

J. Biol. Chem., 290, 4728-4740. (2015)


The pCri system: a vector collection for recombinant protein expression and purification.

T. Goulas, A. Cuppari, R. García-Castellanos, S. Snipas, R. Glockshuber, J.L. Arolas & F.X. Gomis-Rüth.

PLoS ONE, 9, e112643. (2014)


Structure and mechanism of cysteine peptidase Kgp, a major virulence factor of Porphyromonas gingivalis in periodontitis.

I. De Diego, F. Veillard, M.N. Sztukowska, T. Guevera, B. Potempa, A. Pomowski, J.A. Huntington, J. Potempa & F.X. Gomis-Rüth

J. Biol. Chem., 289, 32291-32302. (2014)


Crystallization and preliminary X-Ray diffraction analysis of eukaryotic α2-macroglobulin family members modified by methylamine, proteases and glycosidases.

T. Goulas, I. Garcia-Ferrer, S. García-Piqué, L. Sottrup-Jensen & F.X. Gomis-Rüth

Mol. Oral Microbiol., 29, 354-364. (2014)


Expression and purification of integral membrane metallopeptidase HtpX.

J.L. Arolas, R. García-Castellanos, T. Goulas, Y. Akiyama & F.X. Gomis-Rüth

Prot. Expr. Purif., 99, 113-118. (2014)


Multiple stable conformations account for reversible concentration-depedent oligomerization and autoinhibition of a metamorphic metallopeptidase.
López-Pelegrín, M. Cerdà-Costa, A. Cintas-Pedrola, F. Herranz-Trillo, P. Bernadó, J.R. Peinado, J.L. Arolas & F.X. Gomis-Rüth.

Angew. Chem. Int. Ed., 53, 10624-10630 (2014)

(chosen for the frontispiece of the section on communications).


Architecture and function of metallopeptidase catalytic domains.

N. Cerdà-Costa & F.X. Gomis-Rüth

Prot. Sci., 23, 123-144. (2014)


A novel family of soluble minimal scaffolds provides structural insight into the catalytic domains of integral-membrane metallopeptidases.

M. López-Pelegrín, N. Cerdà-Costa, F. Martínez-Jiménez, A. Cintas-Pedrola, A. Canals, J.R. Peinado, M.A. Martí-Renom, C. López-Otin, J.L. Arolas & F.X. Gomis-Rüth

J. Biol. Chem., 288, 21279-21294. (2013)


Structure-function studies of the staphylococcal methicillin resistance anti-repressor, MecR2.

P. Arêde, T. Botelho, T. Guevera, I. Usón, D.C. Oliveira & F.X. Gomis-Rüth

J. Biol. Chem., 2013; 288, 21267-21278. (2013)


Inhibition of gingipains by their profragments as the mechanism protecting Porphyromonas gingivalis against premature activation of secreted proteases.

F. Veillard, M. Sztukowska, D. Mizgalska, M. Ksiazek, J.A. Houston, B. Potempa, J.J. Enghild, I.B. Thøgersen, F.X. Gomis-Rüth & J. Potempa.

Biochim. Biophys. Acta – Gen. Subj., 1830, 4218-4228. (2013)


Porphyromonas gingivalis virulence factor gingipain RgpB shows a unique zymogenic mechanism for cysteine peptidases.

I. De Diego, F. T. Veillard, T. Guevara, B. Potempa, M. Sztukowska, J. Potempa & F.X. Gomis-Rüth

J. Biol. Chem., 288, 14287-14296. (2013)


Structure of Tannerella forsythia matrix-metallopeptidase karilysin catalytic domain in complex with a tetrapeptidic inhibitor.

T. Guevara, M. Ksiazek, P.D. Skottrup, N. Cerda-Costa, S. Trillo-Muyo, I. de Diego, E. Riise, J. Potempa & F.X. Gomis- Rüth.

Acta Cryst., F69, 472-476. (2013)


Ultra-tight crystal packing of a 10-KDa protein.

S. Trillo-Muyo, A. Jasilionis, M. Domagalski, M. Chruszcz, W. Minor, N. Kuisiene, J.L. Arolas, M. Solà & F.X. Gomis-Rüth (2013).

Acta Cryst., D69, 464-470. (2013)


Mechanism of action of a Janus-faced single-domain protein inhibitor simultaneously targeting two peptidase classes.

S. Trillo-Muyo, S. Martínez-Rodríguez, J.L. Arolas & F.X. Gomis-Rüth

Chem. Sci., 4, 791-797. (2013)


Structural basis for the sheddase function of human meprin β metalloproteinase at the plasma membrane.
J.L. Arolas, C. Broder, T. Jefferson, T. Guevara, E.E. Sterchi, W. Bode, W. Stöcker, C. Becker-Pauly & F.X. Gomis-Rüth.

Proc. Natl. Acad. Sci. USA, 109, 16131-16136. (2012)


Functional and structural insights into astacin metallopeptidases.

F.X. Gomis-Rüth, S. Trillo-Muyo & W. Stöcker

Biol. Chem., 393, 1027-1041. (2012)


A standard orientation for metallopeptidases.

F.X. Gomis-Rüth, T.O. Botelho & W. Bode

Biochim. Biophys. Acta – Prot. & Proteom., 1824, 157-163. (2012)


The crystal structure of human α2-macroglobulin reveals a unique molecular cage.

Marrero, S. Duquerroy, S. Trapani, T. Goulas, T. Guevara, G.R. Andersen, J. Navaza, L. Sottrup-Jensen & F.X. Gomis-Rüth.

Angew. Chem. Int. Ed., 51, 3340-3344 (2012)

(chosen by the journal as a Very Important Paper and for the issue cover; comment in C. Meyer, W. Hinrichs & U. Hahn, Human α2-macroglobulin–another variation on the venus flytrap, Angew. Chem. Int. Ed., 51, 5045-5047).


Structural evidence for standard-mechanism inhibition in metallopeptidases from a complex poised to re-synthesize a peptide bond.
J.L. Arolas, T.O. Botelho, A. Vilcinskas & F.X. Gomis-Rüth. (2011)

Angew. Chem. Int. Ed., 50, 10357-10360.


Structural and functional analyses reveal that Staphylococcus aureus antibiotic resistance factor HmrA is a zinc-depedent endopeptidase

T.O. Botelho, T. Guevara, A. Marrero, P. Arêde, V.S. Fluxà, J.-L. Reymond, D.C. Oliveira & F.X. Gomis-Rüth

J. Biol. Chem., 286, 25697-25709. (2011)


The structure of the catalytic domain of Tannerella forsythia karilysin reveals it is a bacterial xenolog of animal matrix metalloproteinases.

N. Cerdà-Costa, T. Guevara, A.Y. Karim, M. Ksiazek, K.-A. Nguyen, J.L. Arolas,, J. Potempa & F.X. Gomis-Rüth

Mol. Microbiol., 79, 119-132. (2011)


Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog.
T. Goulas, J.L. Arolas & F.X. Gomis-Rüth

Proc. Natl. Acad. Sci. USA, 108, 1856-1861. (2011)


Flexibility of the thrombin-activatable fibrinolysis inhibitor pro-domain enables productive binding of protein substrates.

Z. Valnickova, L. Sanglas, J.L. Arolas, S.V. Petersen, C. Schar, D. Otzen, F.X. Avilés, F.X. Gomis-Rüth & J.J. Enghild

J. Biol. Chem., 285, 38243-38250. (2010)


Structure-function analysis of the short splicing-variant carboxypeptidase encoded by Drosophila melanogaster silver.

S. Tanco, J.L. Arolas, T. Guevara, J. Lorenzo, F.X. Avilés & F.X. Gomis-Rüth

J. Mol. Biol., 401, 465-477. (2010)


Insights into the molecular inactivation mechanism of human activated thrombin-activatable fibrinolysis inhibitor.

L. Sanglas, J.L. Arolas, Z. Valnickova, F.X. Avilés, J.J. Enghild & F.X. Gomis-Rüth

J. Thromb. Haemost., 8, 1056-1065 (2010)

(Comment in the same issue: A. Gils, Hot spots in TAFIa, J. Thromb. Haemost., 8, 1054-1055).


Proenzyme structure and activation of astacin metallopeptidase.

T. Guevara, I. Yiallouros, R. Kappelhoff, S. Bissdorf, W. Stöcker & F.X. Gomis-Rüth.

J. Biol. Chem., 285, 13958-13965. (2010)


On the relevance of the Met-turn methionine in metzincins.

C. Tallant, R. García-Castellanos, U. Baumann & F.X. Gomis-Rüth.

J. Biol. Chem., 285, 13951-13957. (2010)


Matrix metalloproteinases: fold and function of their catalytic domains.

C. Tallant, A. Marrero & F.X. Gomis-Rüth.

Biochim. Biophys. Acta – Mol. Cell Res., 1803, 20-28. (2010)


Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains.

D.R. Boer, J.A. Ruíz-Masó, J.R. López-Blanco, A.G. Blanco, M. Vives-Llàcer, P. Chacón, I. Usón, F. X. Gomis-Rüth, M. Espinosa, O. Llorca, G. del Solar & M. Coll

EMBO J, 28(11):1666-78 (2009)


Macrophage elastase (MMP-12) kills bacteria within murine macrophages.
A.M. Houghton, W.O. Hartzell, C.S. Robbins, F.X. Gomis-Rüth & S.D. Shapiro.

Nature, 460, 637-641. (2009)


Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis.

H. Wójtowicz, T. Guevara, C. Tallant, M. Olczak, A. Sroka, J. Potempa, M. Solà, T. Olczak & F. X. Gomis-Rüth

PLoS Pathog., 5, e1000419. (2009)


Catalytic domain architecture of metzincin metalloproteases.

F.X. Gomis-Rüth

J. Biol. Chem., 284, 15353-15357. (2009)


Purification, crystallization and preliminary X-ray diffraction of wild-type and mutant recombinant human transforming growth factor beta induced protein (TGFBIp).

K. Runager, R. García-Castellanos, Z. Valnickova, T. Kistensen, N.C. Nielsen, G.K. Klintworth, F.X. Gomis-Rüth & J.J. Enghild

Acta Cryst., F65, 299-303. (2009)


Mammalian metallopeptidase inhibition at the defense barrier of Ascaris parasite.

L. Sanglas, F.X. Avilés, R. Huber, F.X. Gomis-Rüth & J.L. Arolas.

Proc. Natl. Acad. Sci. USA, 106, 1743-1747. (2009)


The molecular analysis of Trypanosoma cruzi metallocarboxypeptidase 1 provides insight into fold and substrate specificity.

G. Niemirowicz, D. Fernández, M. Solà, J.J. Cazzulo, F.X. Avilés & F.X. Gomis-Rüth

Mol. Microbiol., 70, 853-866. (2008)


Structure and function of metallocarboxypeptidases

F.X. Gomis-Rüth

Crit. Rev. Biochem. Mol. Biol., 43, 319-345. (2008)


A new autocatalytic activation mechanism for cysteine proteases revealed by Prevotella intermedia interpain A

N. Mallorquí-Fernández, S.P. Manandhar, G. Mallorquí-Fernández, I. Usón, K. Wawrzonek, T. Kantyka, M. Solà, I.B. Thøgersen, J.J. Enghild, J. Potempa & F.X. Gomis-Rüth

J. Biol. Chem., 283, 2871-2882. (2008)


Structure of activated thrombin-activatable fibrinolysis inhibitor, a molecular link between coagulation and fibrinolysis.
Sanglas, Z. Valnickova, J.L. Arolas, I. Pallarés, T. Guevara, M. Solà, T. Kristensen, J.J. Enghild, F.X. Avilés & F.X. Gomis-Rüth.

Mol. Cell, 31, 598-606. (2008)


Activity of ulilysin, an archaeal PAPP-A-related gelatinase and IGBP protease.

C. Tallant, R. García-Castellanos, A. Marrero, F. Canals, Y. Yang, J.L. Reymond, M. Solà, U. Baumann & F.X. Gomis-Rüth.

Biol. Chem, 388, 1243-1253. (2007)


Caught after the act: a human A-type metallocarboxypeptidase in a product complex with a cleaved hexapeptide.

A. Bayés, D. González, M. Solà, A. Marrero, S. García-Piqué, F.X. Avilés, J. Vendrell & F.X. Gomis-Rüth

Biochemistry, 46, 6921-6930. (2007)


 The X-ray crystal structures of two constitutively active mutants of the E. coli  PhoB receiver domain give insights into activation.

R. Arribas-Bosacoma, S.-K. Kim, C. Ferrer-Orta, A.G. Blanco, P.J.B. Pereira, F.X. Gomis-Rüth, B.L. Wanner, M. Coll & M. Solà

J. Mol. Biol., 366, 626-641. (2007)


Substrate specificity of a metalloprotease of the pappalysin family revealed by an inhibitor and a product complex.

R. García-Castellanos, C. Tallant, A. Marrero, M. Solà, U.Baumann & F.X. Gomis-Rüth

Arch. Biochem. Biophys., 457, 57-72. (2007)


Cut and move: Protein machinery for DNA processing in bacterial conjugation.

F. X. Gomis-Rüth & M. Coll

Curr. Op. Struct. Biol., 16, 744-752. (2006)


Papaya glutamine cyclotransferase shows a singular fivefold β-propeller architecture that suggests a novel reaction mechanism.

T. Guevara, N. Mallorquí-Fernández, R. García-Castellanos, S. García-Piqué, G.E. Petersen, C. Lauritzen, J. Pedersen, J. Arnau, F. X. Gomis-Rüth & M. Solà

Biol. Chem., 387, 1479-1486. (2006)


The cofactor-induced pre-active conformation in PhoB.

M. Solà, D.L. Drew, A.G. Blanco, F.X. Gomis-Rüth & M. Coll

Acta Cryst., D62, 1046-1057. (2006)


Unbound and acylated structures of the MecR1 extracellular antibiotic-sensor domain provide insights into the signal-transduction systems that triggers methicillin resistance.

A. Marrero, G. Mallorquí-Fernández, T. Guevara, R. García-Castellanos & F.X. Gomis-Rüth

J. Mol. Biol., 361, 506-521. (2006)


Molecular analysis of ulilysin, the structural prototype of a new family of metzincin metalloproteases.

C. Tallant, R. García-Castellanos, J. Seco, U. Baumann & F.X. Gomis-Rüth

J. Biol. Chem., 281, 17920-17928. (2006)


Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking.

D. Mouradov, A. Craven, J.K. Forwood, J.U. Flanagan, R. García-Castellanos, F.X. Gomis-Rüth, J.L. Martin, B. Kobe & T. Huber

Protein Eng. Des. Sel. (PEDS), 19, 9-16. (2006)


Detailed molecular comparison between the inhibition mode of A/B-type carboxypeptidases in the zymogen state and by the endogenous inhibitor latexin.

R. García-Castellanos, R. Bonet-Figueredo, I. Pallarés, S. Ventura, F.X. Avilés, J. Vendrell & F.X. Gomis-Rüth

Cell. Mol. Life Sci., 62, 1996-2014. (2005)


Identification and characterization of human archaemetzincins-1 and -2, two novel members of a family of metalloproteases widely distributed in archaea.

A. Díaz-Perales, V. Quesada, J.R. Peinado, A. P. Ugalde, J. Álvarez, M.F. Suárez, F.X. Gomis-Rüth & C. López-Otín

J. Biol. Chem., 280, 30367-30375. (2005)


Structure of human carboxypeptidase A4 with its endogenous protein inhibitor, latexin.

I. Pallarés, R. Bonet, R. García-Castellanos, S. Ventura, F.X. Avilés, J. Vendrell & F.X. Gomis-Rüth

Proc. Natl. Acad. Sci. USA, 102, 3978-3983. (2005)


The eight-cysteine motif, a versatile structure in plant proteins.

M. José-Estanyol, F.X. Gomis-Rüth & P. Puigdomènech

Plant Physiol.Biochem., 42, 355-365. (2004)


Staphylococcal methicillin resistance: fine focus on folds and functions.

G. Mallorquí-Fernández, A. Marrero, S. García-Piquè, R. García-Castellanos & F.X. Gomis-Rüth

FEMS Microbiol. Lett., 235, 1-8. (2004)


Coupling factors in macromolecular type IV secretion machineries.

F.X. Gomis-Rüth, M. Solà, F. de la Cruz & M. Coll

Curr. Pharm. Des., 10, 1551-1565. (2004)


On the transcriptional regulation of methicillin resistance: MecI repressor in complex with its operator.

R. García-Castellanos, G. Mallorquí-Fernández, A. Marrero, J. Potempa, M. Coll & F.X. Gomis-Rüth.

J. Biol. Chem., 279, 17888-17896. (2004)


Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC.

A. Guasch, M. Lucas, M. Cabezas, R. Pérez-Luque, F.X. Gomis-Rüth, F. de la Cruz & M. Coll

Nat. Struct. Biol., 10, 1002-1010. (2003)


Three-dimensional structure of MecI: molecular basis for transcriptional regulation of staphylococcal methicillin resistance.

R. García-Castellanos, A. Marrero, G. Mallorquí-Fernández, J. Potempa, M. Coll & F.X. Gomis-Rüth

J. Biol. Chem., 278, 39897-39905. (2003)


Structure of xylanase Xys1Δ from Streptomyces halstedii.

A. Canals, M.C. Vega, F.X. Gomis-Rüth, M. Díaz, R.I. Santamaría & M. Coll

Acta Cryst., D59, 1447-1453. (2003)


Structural aspects of the metzincin clan of metalloendopeptidases.

F. X. Gomis-Rüth

Mol. Biotech., 24, 157-202. (2003)


The matrix protein VP40 from Ebola virus octamerizes into pore-like structures with specific RNA-binding properties.

F. X. Gomis-Rüth, A. Dessen, J. Timmins, A. Bracher, L. Kolesnikowa, S. Becker, H.-D. Klenk & W. Weissenhorn

Structure, 11, 423-433. (2003)


A genetically economical family of plasmid-encoded transcriptional repressors involved in the control of plasmid copy number.

G. del Solar, A.M. Hernández-Arriaga, F.X. Gomis-Rüth, M. Coll & M. Espinosa

J. Bacteriol., 184, 4943-4951. (2002)


Human procarboxypeptidase B: three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI).

P.J.B. Pereira, S. Segura-Martín, B. Oliva, C. Ferrer-Orta, F.X. Avilés, M. Coll, F.X. Gomis-Rüth & J. Vendrell.

J. Mol. Biol., 321, 537-547. (2002)


The structure of human prokallikrein 6 reveals a novel activation mechanism for the kallikrein family.

F.X. Gomis-Rüth, A. Bayés, G. Sotiropoulou, G. Pampalakis, T. Tsetsenis, V. Villegas, F.X. Avilés & M. Coll

J. Biol. Chem., 277, 27273-27281. (2002)


Bacterial conjugation: a two-step mechanism for DNA transport.

M. Llosa, F.X. Gomis-Rüth, M. Coll & F. de la Cruz

Mol. Microbiol.,  45, 1-8. (2002)


Structure and role of coupling proteins in conjugal DNA transfer.

F.X. Gomis-Rüth, F. de la Cruz & M. Coll

Res. Microbiol., 153, 199-204. (2002)


Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator.

A.G. Blanco, M. Solà, F.X. Gomis-Rüth & M. Coll

Structure, 10, 701-713. (2002)

(Comment in Structure Previews by K. Volz).


Conjugative plasmid protein TrwB, an integral membrane type IV secretion system coupling protein: detailed structural features and mapping of the active site cleft.

F.X. Gomis-Rüth, G. Moncalián, F. de la Cruz & M. Coll

J. Biol. Chem., 277, 7556-7566. (2002)


Detailed architecture of a DNA translocation machine: the high resolution structure of bacteriophage Φ29 connector particle.

A. Guasch, J. Pous, B. Ibarra, F.X. Gomis-Rüth, J.M. Valpuesta, N. Sousa, J.L. Carrascosa & M. Coll

J. Mol. Biol., 315, 663-676. (2002)


Trypanosoma cruzi macrophage infectivity potentiator has a rotamase core and a highly exposed α-helix.

P.J.B. Pereira, M.C. Vega, E. González-Rey, R. Fernández-Carazo, S. Macedo-Ribeiro, F. X. Gomis-Rüth, A. González & M. Coll

EMBO Rep., 3, 88-94. (2002)


The structure of TrwB, a gatekeeper in bacterial conjugation.

F.X. Gomis-Rüth & M. Coll

Int. J. Biochem. Cell Biol., 33, 839-843. (2001)


Structure of a membrane DNA transfer protein essential for bacterial conjugation.
F.X. Gomis-Rüth, G. Moncalián, R. Pérez-Luque, A. González, E. Cabezón, F. de la Cruz & M. Coll.

Nature, 409, 637-641. (2001)


Plasmid transcriptional repressor CopG oligomerises to render helical superstructures unbound and in complexes with oligonucleotides.

M. Costa, M. Solà, G. Del Solar, R. Eritja, A.M. Hernández-Arriaga, M. Espinosa, F.X. Gomis-Rüth & M. Coll

J. Mol. Biol., 310, 403-417. (2001)


Solving a 300 kDa multimeric protein by low-resolution MAD phasing and averaging/phase extension.

F.X. Gomis-Rüth & M. Coll

Acta Cryst., D57, 800-805. (2001)


The crystal structure of the inhibitor-complexed carboxypeptidase D domain II as a basis for the modelling of regulatory carboxypeptidases.

P. Aloy, V. Companys, J. Vendrell, F.X. Avilés, L.D. Fricker, M. Coll & F.X. Gomis-Rüth

J. Biol. Chem., 276, 16177-16184. (2001)


The role of Exon 5 in fibroblast collagenase (MMP-1) substrate specificity and inhibitor selectivity.

V. Knäuper, M.L. Stewart, F.X. Gomis-Rüth, B. Smith, A. Lyons, A.J.P. Docherty & G. Murphy

Eur. J. Biochem., 268, 1888-1896. (2001)


Three-dimensional crystal structure of human RNase 1ΔN7 at 1.9 Å.

J. Pous, G. Mallorquí-Fernández, R. Peracaula, S.S. Terzyan, J. Futami, H. Tada, H. Yamada, M. Seno, R. de Llorens, F.X. Gomis-Rüth & M. Coll

Acta Cryst., D57, 498-505. (2001)


Three-dimensional structure of human eosinophil cationic protein (RNase 3) at 1.75 Å resolution.

G. Mallorquí-Fernández, J. Pous, R. Peracaula, T. Maeda, H. Tada, H. Yamada, M. Seno, R. de Llorens, F.X. Gomis-Rüth & M. Coll

J. Mol. Biol., 300, 1297-1309. (2000)


Crystal structure of avian carboxypeptidase D domain II: a prototype for the regulatory metallocarboxypeptidase family.

F.X. Gomis-Rüth, V. Companys, Y. Qian, L.D. Fricker, J. Vendrell, F.X. Avilés & M. Coll

EMBO J., 18, 5817-5826. (1999)


Two wavelength MAD phasing: in search of the optimal wavelengths.

A. González, J.-D. Pédelacq, M. Solà, F.X. Gomis-Rüth, M. Coll, J.P. Samama & S. Benini

Acta Cryst., D55, 1449-1458. (1999)


Three-dimensional crystal structure of the transcription factor PhoB receiver domain.

M. Solà, F.X. Gomis-Rüth, L. Serrano, A. González & M. Coll

J. Mol. Biol., 285, 675-687. (1999)


The three dimensional structure of human RNase 4, unliganded and complexed with d(Up), reveals the basis for its uridine selectivity

S.S. Terzyan, R. Peracaula, R. de Llorens, Y. Tsushima, H. Yamada, M. Seno, F.X. Gomis-Rüth & M. Coll

J. Mol. Biol., 285, 205-214. (1999)


The structure of plasmid-encoded transcriptional repressor CopG, unliganded and bound to its operator.

F.X. Gomis-Rüth, M. Solà, P. Acebo, A. Párraga, A. Guasch, R. Eritja, A. González, M. Espinosa, G. del Solar & M. Coll

EMBO J., 17, 7404-7415. (1998)


Overexpression, purification, crystallization, and preliminary X-ray diffraction analysis of the receiver domain of PhoB.

M. Solà, F.X. Gomis-Rüth, A. Guasch, L. Serrano & M. Coll

Acta Cryst., D54, 1460-1463. (1998)


A novel strategy for inhibition of α-amylases: yellow meal worm α-amylase in complex with the Ragi bifunctional inhibitor at 2.5 Å resolution.

S. Strobl, K. Maskos, G. Wiegand, R. Huber, F.X. Gomis-Rüth & R. Glockshuber

Structure, 6, 911-921. (1998)


Overexpression, purification, crystallization, and preliminary X-ray diffraction analysis of the pMV158-encoded plasmid transcriptional repressor protein CopG.

F.X. Gomis-Rüth, M. Solà, R. Pérez-Luque, P. Acebo, M.T. Alda, A. González, M. Espinosa, G. del Solar & M. Coll

FEBS Lett., 425, 161-165. (1998)


Crystal structure of the yellow meal worm α-amylase at 1.64 Å resolution.

S. Strobl, K. Maskos, M. Betz, G. Wiegand, R. Huber, F.X. Gomis-Rüth & R. Glockshuber

J. Mol. Biol., 278, 617-628. (1998)


Cutting at the right place. The importance of selective limited proteolysis in the activation of proproteinase

F.X. Gomis-Rüth, M. Gómez-Ortiz, J. Vendrell, S. Ventura, W. Bode, R. Huber & F.X. Avilés

Eur. J. Biochem., 251, 839-844. (1998)


Structures of adamalysin II with peptidic inhibitors. Implications for the design of tumour necrosis factor α convertase inhibitors

F.X. Gomis-Rüth, E.F. Meyer, L.F. Kress & V. Politi

Prot. Sci., 7, 283-292. (1998)


Structure of proline iminopeptidase from Xanthomonas campestris pv. citri : a prototype for the prolyl oligopeptidase family.

F.J. Medrano, J. Alonso, J.L. García, A. Romero, W. Bode & F.X. Gomis-Rüth

EMBO J., 17, 1-9. (1998)


2 Å X-ray structure of adamalysin II complexed with a peptide phosphonate inhibitor adopting a retro-binding mode.

M. Cirilli, C. Gallina, E. Gavuzzo, C. Giordano, F.X. Gomis-Rüth, B. Gorini, L.F. Kress, F. Mazza, M. Paglialunga Paradisi, G. Pochetti & V. Politi

FEBS Lett., 418, 319-322. (1997)


Mechanism of inhibition of the human matrix metalloproteinase stromelysin-1 by TIMP-1.
F.X. Gomis-Rüth, K. Maskos, M. Betz, A. Bergner, R. Huber, K. Suzuki, N. Yoshida, H. Nagase, K. Brew, G.P. Bourenkov, H. Bartunik & W. Bode.

Nature, 389, 77-81. (1997)


Expression, purification, characterization and X-ray analysis of selenomethionine 215 variant of leukocyte collagenase.

M. Pieper, M. Betz, N. Budisa, F.X. Gomis-Rüth, W. Bode & H. Tschesche

J. Prot. Chem., 16, 637-650. (1997)


The 1.8-Å crystal structure of the catalytic domain of human neutrophil collagenase (matrix metalloproteinase-8) complexed with a peptidomimetic hydroxamate primed-side inhibitor with a distinct selectivity profile.

M. Betz, P. Huxley, S.J. Davies, Y. Mushtaq, M. Pieper, H. Tschesche, W. Bode & F.X. Gomis-Rüth

Eur. J. Biochem., 247, 356-363. (1997)


The α-amylase from the yellow meal worm: complete primary structure, crystallization and preliminary X-ray analysis.

S. Strobl, F.X. Gomis-Rüth, K. Maskos, G. Frank, R. Huber & R. Glockshuber

FEBS Lett., 409, 109-114. (1997)


Crystal structure of an oligomer of proteolytic zymogens: detailed conformational analysis of the bovine ternary complex and implications for their activation.

F.X. Gomis-Rüth, M. Gómez-Ortiz, J. Vendrell, S. Ventura, W. Bode, R. Huber & F.X. Avilés

J. Mol. Biol., 269, 861-880. (1997)


Pancreatic procarboxypeptidases: oligomeric structures and activation processes revisited.

S. Ventura, F.X. Gomis-Rüth, A. Puigserver, F.X. Avilés & J. Vendrell

Biol. Chem., 378, 161-165. (1997)


Crystal structures of modified apo-His117Gly and apo-His46Gly mutants of Pseudomonas aeruginosa azurin.

C. Hammann, G. van Pouderoyen, H. Nar, F.X. Gomis-Rüth, A. Messerschmidt, R. Huber, T. den Blaauwen & G.W. Canters

J. Mol. Biol., 266, 357-366. (1997)


The inhibition of carboxypeptidase A by excess zinc: analysis of the structural determinants by X-ray crystallography.

M. Gómez-Ortiz, F.X. Gomis-Rüth, R. Huber & F.X. Avilés

FEBS Lett., 400, 336-340. (1996)


Crystallization and preliminary X-ray diffraction analysis of proline-iminopeptidase from Xanthomonas campestris pv. citri.

F.J. Medrano, J. Alonso, J.L. García, W. Bode & F.X. Gomis-Rüth

FEBS Lett., 400, 91-93. (1996)


The helping hand of collagenase 3 (MMP-13): 2.7 Å crystal structure of its C-terminal haemopexin-like domain.

F.X. Gomis-Rüth, U. Gohlke, M. Betz, V. Knäuper, G. Murphy, C. López-Otín & W. Bode.

J. Mol. Biol., 264, 556-566. (1996)


Protein crystal density by volume measurement and amino acid analysis.

R. Kiefersauer, J. Stetefeld, F.X. Gomis-Rüth, M.J. Romão, F. Lottspeich & R. Huber

J. Appl. Crystallogr., 29, 311-317. (1996)


The C-terminal (haemopexin-like) domain structure of human gelatinase A (MMP2): structural implications for its function.

U. Gohlke, F.X. Gomis-Rüth, T. Crabbe, G. Murphy, A.J.P. Docherty & W. Bode

FEBS Lett., 378, 126 -130. (1996)


The three-dimensional structure of the native ternary complex of bovine pancreatic procarboxypeptidase A with proproteinase E and chymotrypsinogen C.

F. X. Gomis-Rüth, M. Gómez, W. Bode, R. Huber & F. X. Avilés

EMBO J., 14, 4387-4394. (1995)


Determination of hemihedral twinning and initial structural analysis of crystals of the procarboxypeptidase A ternary complex.

F.X. Gomis-Rüth, I. Fita , R. Kiefersauer, R. Huber , F.X. Avilés & J. Navaza

Acta Cryst., D51, 819-823. (1995)


Crystallization and preliminary X-ray analysis of the ternary complex of procarboxypeptidase A from bovine pancreas.

F. X. Gomis-Rüth, M. Gómez, S. Ventura, J. Vendrell & F. X. Avilés

FEBS Lett., 367, 211-213. (1995)


The metzincins – Topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases.

W. Stöcker, F. Grams, U. Baumann, P. Reinemer, F.X. Gomis-Rüth, D.B. McKay & W. Bode

Prot. Sci., 4, 823-840. (1995)


Structural interaction of natural and synthetic inhibitors with the venom metalloproteinase, atrolysin C (form d).

D. Zhang, I. Bothos, F.X. Gomis-Rüth, R. Doll, C. Blood, F.G. Njoroge, J.W. Fox, W. Bode & E.F. Meyer

Proc. Natl. Acad. Sci. USA, 91, 8447-8451.  (1994)


Refined 2.0 Å X-ray crystal structure of the snake venom zinc-endopeptidase adamalysin II. Primary and tertiary structure determination, refinement, molecular structure and comparison with astacin, collagenase and thermolysin.

F.X. Gomis-Rüth, L.F. Kress, J. Kellermann, I. Mayr, X. Lee, R. Huber & W. Bode

J. Mol. Biol., 239, 513-544. (1994)


Crystal structures, spectroscopic features and catalytic properties of cobalt(II), copper(II), nickel(II), and mercury(II) derivatives of the zinc endopeptidase astacin. A correlation of structure and proteolytic function.

F.X. Gomis-Rüth, F. Grams, I. Yallouros, H. Nar, U. Küsthardt, R. Zwilling, W. Bode & W. Stöcker

J. Biol. Chem., 269, 17111-17117. (1994)


First structure of a snake venom metalloproteinase: a prototype for matrix metalloproteinases/collagenases.

F.X. Gomis-Rüth, L.F. Kress & W. Bode

EMBO J., 12, 4151-4157. (1993)


Astacins, serralysins, snake venom and matrix metalloproteinases exhibit identical zinc-binding environments (HEXXHXXGXXH and Met-turn) and topologies and should be grouped into a common family, the ´metzincins´.

W. Bode, F.X. Gomis-Rüth & W. Stöcker

FEBS Lett., 331, 134-140. (1993)


Implications of the three-dimensional structure of astacin for the structure and function of the astacin family of zinc-endopeptidases.

W. Stöcker, F.X. Gomis-Rüth, W. Bode & R. Zwilling

Eur. J. Biochem., 214, 215-231. (1993)


Refined 1.8 Å X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. Structure determination, refinement, molecular structure, and comparison with thermolysin.

F.X. Gomis-Rüth, W. Stöcker, R. Huber, R. Zwilling & W. Bode

J. Mol. Biol., 229, 945-968. (1993)


Escherichia coli dihydrodipicolinate synthase. Identification of the active site and crystallization.

B. Laber, F.X. Gomis-Rüth, M.J. Romão & R. Huber

Biochem. J., 288, 691-695. (1992)


Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. at 2.0 Å resolution.

M.J. Romão, D. Turk, F.X. Gomis-Rüth, R. Huber, G. Schumacher, H. Möllering & L. Rüssmann

J. Mol. Biol., 226, 1111-1130. (1992)


Structure of astacin and implications for activation of astacins and zinc-ligation of collagenases.

W. Bode, F.X. Gomis-Rüth, R. Huber, R. Zwilling & W. Stöcker

Nature, 358, 164-167. (1992)


Atropoisomería en la serie 11H -dibenzo[b,e]azepínica. Parte III. 11-oxo derivados N-aril sustituidos.

J. Irurre, F. Marquillas, E. Narbón, C. Puig & X. Gomis

An. Quim., 88, 601-606. (1992)

Book chapters


α2-Macroglobulins: structure and function

I. Garcia-Ferrer, A. Marrero, F.X. Gomis-Rüth & T. Goulas (J.R. Harris & J. Marles-Wright, eds.)

In Macromolecular Protein Complexes, 2017.  Subcellular Biochemistry series, Vol. 83 , Springer, Cham (Switzerland), pp. 149-183.


A traves del cristal: Cómo la cristalografía ha cambiado la vision del mundo

F. X. Gomis-Rüth (M. Martínez-Ripoll, J.A. Hermoso & A. Albert, eds.)

Peptidasas: nanomáquinas para el procesado de proteínas, 2014. Los Libros de la Catarata, CSIC, Madrid, pp. 89-97.


Astacins: proteases in development and tissue differentiation

W. Stöcker & F. X. Gomis-Rüth (K. Brix & W. Stöcker, eds.)

Proteases: Structure and Function, 2013. Springer Verlag, Vienna (Austria), pp. 235-263.


Zinc metallocarboxypeptidases

J.L. Arolas & F. X. Gomis-Rüth (V.N. Uversky, R.H. Kretsinger & E.A. Permyakov, eds.)

Encyclopedia of Metalloproteins, 2013. Springer Verlag, Heidelberg, pp. 2473-2479


Zinc adamalysins

F. X. Gomis-Rüth (V.N. Uversky, R.H. Kretsinger & E.A. Permyakov, eds.)

Encyclopedia of Metalloproteins, 2013. Springer Verlag, Heidelberg, pp. 2345-2349 .


185 Karilysin

J. Potempa, F. X. Gomis-Rüth & A.Y. Karim (N.D. Rawlings & G.S. Salvesen, eds.)

Handbook of Proteolytic Enzymes, 2013, Academic Press, Oxford, pp. 883-886 .


186 Fragilysin

T. Goulas & F. X. Gomis-Rüth (N.D. Rawlings & G.S. Salvesen, eds.)

Handbook of Proteolytic Enzymes, 2013, Academic Press, Oxford, pp. 887-891


270 Ulilysin (Methanosarcina acetivorans)

U. Baumann & F. X. Gomis-Rüth (N.D. Rawlings & G.S. Salvesen, eds.)

Handbook of Proteolytic Enzymes, 2013, Academic Press, Oxford, pp. 1208-1211


291 Carboxypeptidase A4

L.D. Fricker & F. X. Gomis-Rüth (N.D. Rawlings & G.S. Salvesen, eds.)

Handbook of Proteolytic Enzyme, 2013. Academic Press, Oxford, pp. 1307-1310


373 HmrA peptidase

T.O. Botelho & F. X. Gomis-Rüth (N.D. Rawlings & G.S. Salvesen, eds.)

Handbook of Proteolytic Enzymes, 2013, Academic Press, Oxford, pp. 1651-1654


Em cura la grip: L’estructura tridimensional de proteïnes com a motlle per el desenvolupament de fàrmacs.

F. X. Gomis-Rüth & M. Solà (Sílvia Pujals Riatós & Eduardo Sabidó Aguadé, eds.)

Què fa la biotecnologia per a mi?, 2010. Xarxa de Referència en Biotecnologia, Generalitat de Catalunya, pp.27-36 (e-Book chapter).


Atomic structure of a molecular switch for blood coagulation and fibrinolysis.

L. Sanglas, Z. Valnickova, J.L. Arolas, I. Pallarés, T. Guevara, M. Solà, T. Kristensen, J.J. Enghild, F.X. Avilés & F.X. Gomis-Rüth (Gary Admans, ed.)

ESRF Highlights 2008, 2009 ESRF, Grenoble, pp.66-67


Hemopexin Domains

F. X. Gomis-Rüth (W. Bode, M. Cygler & A. Messerschmidt, eds.)

Handbook of Metalloproteins – Volume III, 2004, John Wiley & Sons, Chichester, pp. 631-646


Structural basis for the function of astacin and related zinc peptidases

W. Stöcker, I. Yallouros, D. Köhler, S. Gredel, R. Zwilling, V. Dive, W. Bode, F.X. Gomis-Rüth& F. Grams (W. Stöcker & R. Zwilling, eds.).

The Astacins – Structure and Function of a New Protein Family, 1997. Verlag Dr. Kovac, Hamburg, pp. 147-163


Comparison of the crystallographic structure of rattlesnake venom adamalysin II with other members of the metzincin-superfamily of metalloendopeptidases and thermolysin

F.X. Gomis-Rüth, W. Stöcker & W. Bode (W. Stöcker & R. Zwilling, eds.)

The Astacins – Structure and Function of a New Protein Family, 1997. Verlag Dr. Kovac, Hamburg, pp. 329-348.


The metzincins: a new superfamily of zinc endopeptidases.

W. Bode, F. Grams, P. Reinemer, F.X. Gomis-Rüth, U. Baumann, D.B. McKay & W. Stöcker (W. Stöcker & R. Zwilling, eds.)

The Astacins – Structure and Function of a New Protein Family, 1997. Verlag Dr. Kovac, Hamburg, pp. 29-43.

 

Other Publications


Mechanistic insights into the action of a bacterial protease inhibitor (P35-019). 

I. Garcia-Ferrer, P. Arêde-Rei, T. Goulas & F.X. Gomis-Rüth.

FEBS J., 282 (Suppl. 1), 328-328 (Published conference abstract). (2015)


Molecular plasticity controls proteolytic activity.

M. López-Pelegrín, N. Cerdà-Costa, A. Cintas-Pedrola, F. Herranz-Trillo, P. Bernadó, J.R. Peinado, J.L. Arolas & F.X. Gomis-Rüth 

ALBA Activity Report 2014, Alba Synchrotron, Cerdanyola del Vallès (Barcelona), pp. 15-16 (Annual report of activity). (2015)


A different look for AB5 toxins.

F. X. Gomis-Rüth.

Structure, 21, 1909-1910 (Preview of an article in the same issue). (2013)


Structural features of the replication initiator protein RepB of the promiscuous plasmid pMV158. 

J.A. Ruiz-Maso, D.R. Boer, J.R. López-Blanco, A.G. Blanco, M. Vives-Llacer, P. Chacón, I. Usón, F.X. Gomis-Rüth, M. Espinosa, O. Llorca, G. del Solar & M. Coll.

FEBS J., 276 (Suppl. 1), 387-387 (Published conference abstract). (2009)


Biochemical and structural characterisation of human ECI and its complex with human carboxypeptidase A4.

I. Pallarés, R. Bonet, R. García-Castellanos, S. Ventura, F.X. Avilés, J. Vendrell & F.X. Gomis-Rüth

FEBS J., 272 (Suppl. 1), 96-97 (Published conference abstract; poster A2-064P). (2005)


Resistencia bacteriana a los antibióticos.

F. X. Gomis-Rüth & Miquel Coll. Diario de Sevilla, 15-03-2001, pp. 48-49 (Newspaper article).


Insights into MMP-TIMP interactions.

W. Bode, C. Fernández-Catalán, F. Grams, F.X. Gomis-Rüth, H. Nagase, H. Tschesche & K. Maskos.

Ann. N.Y. Acad. Sci., 878, 73-91 (Published conference abstract). (1999)


Cristal.lografia de proteines.

A. Guasch, N. Verdaguer, F.X. Gomis-Rüth, I. Fita & M. Coll

Treballs de la Societat Catalana de Biologia, 48, 13-23 (Special issue of the Catalan Biological Society). (1998).


The metzincin-superfamily of zinc-peptidases. In Intracellular Protein Catabolism

W. Bode, F. Grams, P. Reinemer, F.X. Gomis-Rüth, U. Baumann, D.B. McKay & W. Stöcker (K. Suzuki & J.S. Bond, eds.)

Book Series Advances in Experimental Medicine and Biology, Vol. 389, Plenum Publishing Co., New York, pp. 1 – 11 (Published conference abstract). (1996)


The metzincins: a superfamily of structurally related metalloproteinases.

W. Bode, F. Grams, P. Reinemer, F.X. Gomis-Rüth, U. Baumann, D.B. McKay & W. Stöcker

Zoology – Analysis of Complex Systems, 99, 237-246 (Published conference abstract). (1995/1996)


The crystal structure of adamalysin II, a zinc-endopeptidase from the snake venom of the Eastern diamondback rattlesnake Crotalus adamanteus.

W. Bode, L. Kress & F.X. Gomis-Rüth

Brazilian J. Med. Biol. Res., 27, 2049-2068 (Published conference abstract). (1994)


The three-dimensional structure of astacin: implications for the structure of astacins and for the zinc ligation of other metalloproteinases.

W. Bode, F.X. Gomis-Rüth, R. Zwilling & W. Stöcker

In Proteolysis and Protein Turnover (A.J. Barrett & J.S. Bond, eds.), Portland Press Inc., Cambridge, pp. 13-24 (Published conference abstract). (1993).


Kinetic investigation and X-ray structure analysis of metal-substituted derivatives of the zinc-endopeptidase astacin reveals a correlation between metal-ligand geometry and catalytic activity.

S. Stöcker, I. Yallouros, R. Zwilling, F.X. Gomis-Rüth, F. Grams & W. Bode

Biol. Chem. Hoppe-Seyler, 374, 682-683 (Published conference abstract). (1993)


Biochemische und kristallographische Arbeiten an zwei Enzymen: Dihydrodipicolinat-Synthase und Astacin.

F.X. Gomis-Rüth

Faculty of Chemistry and Pharmacy, University Ludwig-Maximilian, Munich (Germany) (Ph.D.-Thesis). (1992).


Astacin: Archetype of a novel protein-family.

S. Stöcker, F.X. Gomis-Rüth, R. Huber, R. Zwilling & W. Bode

Verh. Dtsch. Zool. Ges.,85, 170-170 (Published conference abstract) (1992)


The three-dimensional structure of astacin and its implications for the structure and function of a new family of zinc-endopeptidases.

S. Stöcker, F.X. Gomis-Rüth, R. Huber, R. Zwilling & W. Bode

Biol. Chem. Hoppe-Seyler, 373, 654-654 (Published conference abstract). (1992)


Síntesis, resolución en atropoisómeros y análisis conformacional en derivados 11-carboximetilénicos de 11H-dibenzo[b,e]azepin-6-onas y 6-tionas N-substituidas.

F.X. Gomis-Rüth

Department of Organic Chemistry, Chemistry Institute of Sarrià (IQS), Barcelona (Spain) (M.Sc.-Thesis) (1989).


Project Funding

Ongoing Projects


Reference: MDM-2014-0435

Title: Appointment of the Department of Structural Biology of IBMB as a “María de Maeztu Unit of Excellence”

Total awarded: €2,000,000 (1.7.2015 – 30.6.2019)

Role: co-PI (out of just 7 PIs)

Spanish Ministry of Economy and Competitivity.


Reference: BFU2015-64487-R

Title: Biochemistry of proteolysis: function, regulation and structure of peptidases of biomedical relevance and their inhibitors

Total awarded: €340,000 (1.1.2016-31.12.2019)

Role: PI

R&D project, State Plan, section Molecular and Cellular Biology, Ministry of Economy and Competitivity


Project Funding

Concluded Projects

(last 5 years)


Reference: FP7-PEOPLE-2011-290246 “RAPID”

Title: RAPID-Rheumatoid arthritis and periodontal inflammatory disease

Total awarded to subgroup: €380,367 (1.4.2013 – 31.3.2017)

Role: Co-PI and Coordinator of Subproject (WP) nº 6 (Coordinator: Thomas Dietrich (Birmingham, UK)

European Union Marie Curie Initial Training Network (ITN) Project


Reference: FP7-HEALTH-2012-306029-2 “TRIGGER”

Title: King of hearts, joints and lungs; periodontal pathogens as etiologic factor in RA, CVD and COPD and their impact on treatment strategies

Total awarded: €519,041 (1.4.2013 – 31.3.2017)

Role: Co-PI and Coordinator of Subproject (WP) nº 6

European Union STREP FP7 Project


Reference: 2014SGR9

Title: Proteolysis Lab

Total awarded: €15,000 (2014 – 2016)

Role: Coordinator

Consolidated Research Groups of Catalunya Grant, Generalitat of Catalunya.


Reference: BIO2013-49320-EXP

Title: Redesign of therapeutic proteins with enhanced stability through incorporation of non-natural amino acids

Total awarded: €60,000 (1.9.2014-31.8.2016,extended to 31.1.2017)

Role: PI

R&D project, State Plan, program Explora technology, section Biotechnology, Ministry of Economy and Competitivity.


Reference: CSD2006-00015

Title: The Crystallization Factory

Total awarded: €5,000,000. Grant awarded to subgroup: €171,308 (6.12.2006-6.12.2014)

Role: Co-PI (coordinator: J.M. García Ruiz)

“Consolider-Ingenio” Project 2010, first call (2006). Ministry of Education and Science.


Reference: FP7-HEALTH-2010-261460 “Gums&Joints”

Title: Protein citrullination as a link between periodontal diseases and rheumatoid arthritis (RA) and target for development of novel drugs to treat RA

Grant awarded to subgroup: €504,510 (1.11.2010 – 31.10.2014)

Role: Co-PI and Coordinator of Subproject (WP) nº 3 (coordinator: Peter Mydel; Bergen, Norway)

European Union STREP FP7 Project


Reference: “Fundació La Marató de TV3” Research Project 100732

Title: Clinical, genetic, epidemiological, pathophysiological and translational studies of spinocerebellar ataxias

Grant awarded to subproject: €176,500 (1.1.2011 – 30.6.2014, after 6-month extension)

Role: Co-PI (coordinator: Antoni Matilla Dueñas; IICSGTP, Badalona)

“Fundació La Marató de TV3” Research Project, Edition 2009 – Biomedical Research Projects in Minority Diseases.


Reference: 2009SGR1036

Title: Structural biology: computational methods and structure-function analysis of proteins of biomedical and biotechnological interest (MEBIO)

Total awarded: €42,640 (2009 – 2013, extended until 31.3.2014)

Role: Coordinator and co-PI.

Consolidated Research Groups of Catalunya Grant, Generalitat of Catalunya.


Reference: 210RT0390

Title: Multidisciplinary network for the study of disorders of movement: Parkinson’s disease and spinocerebellar ataxias

Total awarded: €128,000 (2009 – 2013)

Role: Co-PI.

Programme for the Development of Science and Technology in Latin-American (CYTED).


Reference: FP7-HEALTH-F3-2009-223101 “AntiPathoGN”

Title: Identification and validation of novel drug targets in Gram-negative bacteria by global search: a trans-system approach

Grant awarded to subgroup: €300,000 (1.2.2009 – 30.6.2013, after 6-month extension)

Role: Co-PI, Responsible for the Third Part of Subproject nº 2 (coordinator: Xavier Daura; UAB, Barcelona)

European STREP FP7 Project


Reference: BIO2009-10334

Title: Structural biology of hydrolases of therapeutic interest (IV)

Total awarded: €295,000. (1.1.2010-31.12.2012)

Role: PI.

R&D project, National Biotechnology Plan, Ministry of Science and Technology.


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