Astacin

Astacin (1992)

Metallopeptidase (MP) isolated from the digestive fluid of the European freshwater crayfish Astacus astacus. First structure of a MP since thermolysin (1972). Prototype for the astacin family and the metzincin clan of MPs.

Carried out in the laboratories of Robert Huber and Robert Zwilling.

Adamalysin II

Adamalysin II (1993)

MP from crotalid snake venom (left). Prototype for another family of zinc-dependent MPs, the adamalysins, also known as ADAMs, reprolysins or fertilysins. These studies were later complemented with inhibitor-bound structures.

Carried out in the laboratories of Robert Huber and Lawrence Kress.

Procarboxypeptidase A ternary complex

Procarboxypeptidase A ternary complex (1995)

The metalloexopeptidase carboxypeptidase A, founding member of the funnelin tribe of MPs, is naturally secreted in ruminants as a zymogen in a ternary complex with two serine proproteinases, chymotrypsinogen C and proproteinase E.

Carried out in the laboratories of Robert Huber, Carlos López-Otín and Gillian Murphy.

Human neutrophil collagenase

Human neutrophil collagenase (MMP-8) inhibitor complex (1997)

The zinc-dependent catalytic domain of collagenase-2 of the MMP family in complex with a potential drug lead compound from British Biotech revealed the structural determinants of inhibition.

Carried out in the laboratories of Robert Huber, British Biotech Pharmaceuticals (Oxford, UK), and Harald Tschesche.

MMP 3 TIMP 1

Complex of stromelysin-1 (MMP-3) with tissue-inhibitor of metalloproteinases 1 (TIMP-1)(1997)

The long awaited first complex structure of a MMP catalytic domain with an endogenous inhibitor of matrixins, TIMP-1.

Carried out in the laboratories of Robert Huber, Hideaki Nagase, Keith Brew and Hans Bartunik.

Prolyl iminopeptidase

Prolyl iminopeptidase (1998).

This serine-dependent aminopeptidase from Xanthomonas campestris displays preference for proline residues at the N-termini of substrates. The enzyme belongs to the α/β hydrolase-fold family, further encompassing prolyl oligopeptidase and dipeptidyl peptidase IV.

Carried out in the laboratories of Robert Huber, José L. García and Antonio Romero.

Tenebrio molitor α amylase

Tenebrio molitor α-amylase (1998)

This amylase from the yellow meal worm comprises 471 residues and its structure was the first representative of an insect α-amylase to be solved. Due to the great importance of the Tenebrio beetle as a cosmopolitan pest of stored products, this enzyme represents a valuable target for drug design.

Carried out in the laboratories of Robert Huber and Rudi Glockshuber.

Tenebrio molitor α amylase inhibitor

Tenebrio molitor α-amylase in complex with Ragi inhibitor (1998)

Complex structure with the bifunctional trypsin and α-amylase inhibitor from Ragi cereal.

Carried out in the laboratories of Robert Huber and Rudi Glockshuber.

Duck carboxypeptidase D

Duck carboxypeptidase D domain II (1999)

The first structure of a regulatory metallocarboxypeptidase of the funnelin tribe of metallopeptidases, in this case from duck, unveiled, in addition to an α/β-hydrolase funnelin domain, a downstream ~80 residue domain reminiscent of transthyretin. The enzyme has preference for positively charged C-termini in substrates. The whole enzyme evinces three such tandem repeats and the one solved for its structure was the second. A complex with a small-molecule inhibitor (GEMSA) allowed to map the active site with detail.

Carried out in the laboratories of Miquel Coll, Francesc X. Avilés, and Lloyd D. Fricker.

Human prokallikrein 6

Human prokallikrein 6 (2002)

The first structure of a human prokallikrein family member, a trypsin-like serine proproteinase, unveiled a novel activation mechanism, when compared with neurosin (chosen as model for the active enzyme) but also with the some weeks before published structure of active kallikrein 6 (Bernett et al.(2002), J. Biol. Chem., 277, 24562-24570).

Carried out in the laboratories of Miquel Coll, Francesc X. Avilés and Giorgia Sotiropoulou.

Human procarboxypeptidase B

Human procarboxypeptidase B (2002)

This pancreatic procarboxypeptidase of the funnelin tribe displays type B specificity and its structure allowed homology modelling of TAFI, thrombin-activatable fibrinolysis inhibitor.

Carried out in the laboratories of Miquel Coll at IBMB (Barcelona, Spain) and Francesc X. Avilés.

Human carboxypeptidase A4 latexin

Matrix protein VP40 from Ebola virus (2003)

This viral membrane-associated protein is required for assembly and budding of viral particles. It forms an octameric pore and is capable of selectively binding a RNA triribonucleotide of sequence 5′-U-G-A-3′.

Carried out in the laboratory of Winfried Weissenhorn.

Human carboxypeptidase A4

Human carboxypeptidase A4 in complex with latexin (2005)

This was the first structure of a complex of a human vertebrate funnelin with an endogenous inhibitor.

Carried out in the Proteolysis Lab in collaboration with the laboratory of Francesc X. Avilés.

Human carboxypeptidase A4

Human procarboxypeptidase A4 (2005)

This member of the pancreatic funnelins has been found overexpressed in pancreatic cancer cell lines as a downstream effect of treatment with histone deacetylase inhibitors.

Carried out in the Proteolysis Lab in collaboration with the laboratory of Francesc X. Avilés.

Ulilysin

Methanosarcina acetivorans ulilysin (2006)

The first structure of a novel metzincin structural prototype, ulilysin from Methanosarcina acetivorans, provided a model for the catalytic domain of the pappalysin family. A complex with a small-molecule inhibitor (batimastat) allowed to map the active site with detail.

Carried out in the Proteolysis Lab and in the lab of Ulrich Baumann.

MecR1 penicillin binding domain

Straphylococcus aureus (MRSA) MecR1 penicillin-binding domain, MecR1-PBD (2006)

The structure of the extracellular sensor domain of MecR1, part of a signal-transduction system that triggers methicillin resistance against β-lactam antibiotics in Staphylococcus aureus, was solved isolated and with the active-site serine acylated with oxacillin and penicillin.

Carried out in the Proteolysis Lab.

Human carboxypeptidase A4 product

Human carboxypeptidase A4 product complex (2007)

We serendipitously obtained a complex of this enzyme with a cleaved hexapeptide coming from the pro-domain. This was the first time a true product complex was obtained for a funnelin.

Carried out in the Proteolysis Lab in collaboration with the laboratory of Francesc X. Avilés.

Interpain A

Prevotella intermedia Interpain A (2008)

The structural analysis of the zymogen and the active form of this cysteine protease from the bacterial odontopathogen, Prevotella intermedia, unexpectedly revealed a completely novel activation mechanism entailing major structural rearrangement.

Carried out in the Proteolysis Lab in collaboration with the laboratory of Jan Potempa.

TAFIa funnelin inhibitor

TAFIa in complex with a funnelin inhibitor from tick (TCI) (2008)

The long awaited structure of thrombin-activatable fibrinolysis inhibitor, which could be stabilised by means of a complex with a tight-binding inhibitor.

Carried out in the Proteolysis Lab in collaboration with the laboratories of Francesc X. Avilés and Jan J. Enghild.

Trypanosoma cruzi metallocarboxypeptidase 1

Trypanosoma cruzi metallocarboxypeptidase 1 (2008)

First structure of a protozoan member of the cowrin family of MPs. Most cowrins possess carboxypeptidase or peptidyl dipeptidase activity and the most relevant family member is angiotensin-converting enzyme.

Carried out in the Proteolysis Lab in collaboration with the laboratories of Francesc X. Avilés and Juan J. Cazzulo.

Human-carboxypeptidase A4 ascaris inhibitor

Human carboxypeptidase A1 in complex with an Ascaris inhibitor (ACI) (2009)

This complex structure described a novel funnelin inhibitor isolated from the intestinal parasite, Ascaris suum, and its working mechanism on a potential pancreatic target enzyme in vivo.

Carried out in the Proteolysis Lab in collaboration with the laboratory of Francesc X. Avilés.

Proastacin

Proastacin (2010)

This high-resolution structure enabled us to understand the structural determinants of latency in astacin 18 years after publication of the mature enzyme structure.

Carried out in the Proteolysis Lab in collaboration with the group of Walter Stöcker.

Human TAFIa TCI

Human TAFIa in complex with TCI (2010)

Human pendant of the bovine complex structure.

Carried out in the Proteolysis Lab in collaboration with the laboratories of Francesc X. Avilés and Jan J. Enghild.

Bovine TAF funnelin inhibitor

Bovine TAFI in complex with a funnelin inhibitor from tick (TCI) (2010)

The structure of the zymogen complex of TAFI with TCI revealed that the inhibitor displaces the pro-domain, which is disordered in the structure.

Carried out in the Proteolysis Lab in collaboration with the laboratories of Francesc X. Avilés and Jan J. Enghild.

Catalytic domain Kly18

Tannerella forsythia karilysin catalytic domain Kly18 (2011)

The structure of the first bacterial MMP catalytic domain.

Carried out in the Proteolysis Lab and in the laboratory of Jan Potempa.

Profragilysin 3

Bacteroides fragilis profragilysin-3 (2011)

Structure and function analysis of the only molecular virulence factor of enteropathogenic B. fragilis (ETBF).

Carried out in the Proteolysis Lab.

Methicillin resistance factor HmrA

Staphylococcus aureus (MRSA) methicillin resistance factor HmrA (2011)

Structure and function analysis of a tetrameric molecule responsible for Eagle-type resistance in staphylococci.

Carried out in the Proteolysis Lab in collaboration with the laboratory of Duarte C. Oliveira.

Bacillus thermoproteolyticus thermolysin IMPI

Bacillus thermoproteolyticus thermolysin in complex with IMPI (2011)

The structure of the first complex of a highly specific protein inhibitor of thermolysin isolated from insect also revealed the structuiral details of the first case of standard-mechanism inhibition for MPs.

Carried out in the Proteolysis Lab in collaboration with the group of Andreas Vilcinskas.

Methylamine activated α2 macroglobulin

Human methylamine-activated α2-macroglobulin (2012)

First long-seeked for structure to 4.3Å resolution of a universal pan-proteinase inhibitor from blood plasma.

Carried out in the Proteolysis Lab in collaboration with the laboratories of Lars Sottrup-Jensen, Gregers Andersen, and Jorge Navaza. Stephane Duquerroy and Stefano Trapani also played vital roles in the project.

Meprin β zymogen

Human meprin β and its zymogen (2012)

The multi-domain structure of this astacin-family member plays a major role as sheddase at the plasma membrane. Substrates include amyloid-β precursor proteins but also several cytokines and growth factors. The structures of the mature enzyme and of the zymogen provided insight into the activation mechanism and into its modus operandi in front of membrane-bound substrates.

Carried out in the Proteolysis Lab in collaboration with the groups of Walter Stöcker and Christoph Becker-Pauly.

Streptomyces caespitosus sermetstatin

Streptomyces caespitosus sermetstatin (2013)

This was the first structural report of a Janus-faced protein inhibitor simultaneously targeting endopeptidases from two distinct classes (serine peptidases and metallopeptididases) through a single domain. Based on the isolated homodimeric structure and the two tetrameric (2+2) complexes with subtilisin and S. caespitosus snapalysin, respecively, we could reconstruct the hexameric (2+2+2) complex.

Carried out in the Proteolysis Lab.

U32 peptidase

C-terminal domain of putative U32 peptidase from Geobacillus thermoleovorans (2013)

MEROPS database family U32 groups hypothetic peptidases that follow an unknown mechanism. While trying to crystallize the ortholog from G. thermoleovorans, we seredipitously crystallized its C-terminal non-catalytic domain only, which gave rise to one of the most tightly-packed protein crystals ever described, with just 24,5% of solvens. One monomer of this 10-kDa protein is shown in yellow surrpunded by its crystallographic neighbors.

Carried out in the Proteolysis Lab in collaboration with the Structural MitoLab and the groups of Nomeda Kuisiene, Wladek Minor.

Prophyromonas gingivalis RgpB

Prophyromonas gingivalis RgpB in complex with its pro-domain (2013)

We managed to solve the structure of mature RgpB, a cysteine peptidase that is a major odontopathogenic virulence factor during P. gingivalis infection of the human gums, with its pro-domain. This work revealed a novel mechanism of latency maintenance in peptidases.

Carried out in the Proteolysis Lab in collaboration with the group of Jan Potempa.

Proabylysin projannalysin

Pyrococcus abyssi proabylysin and Methanococcus jannaschii projannalysin (2013)

On the search for minimal metallopeptidases, we came across a family of just ~100-residue proteins, which we termed minigluzincins. We solved the zymogenic structures of the orthologs from Pyrococcus abyssi (pink ribbon) and Methanococcus jannaschii (tan ribbon).

Carried out in the Proteolysis Lab in collaboration with the groups of Carlos López-Otín and Marc A. Martí-Renom.

Methanococcus jannaschiiselecase

Methanococcus jannaschii selecase (2014)

Selecase is the smallest described active MP (110-residues) and it is very selective. It is a metamorphic protein capable of adopting several conformations, out of which only one is monomeric and active.

Carried out in the Proteolysis Lab in collaboration with the group of P. Bernadó.

Porphyromonas gingivalis Kgp

Porphyromonas gingivalis Kgp (2014)

We succeeded in solving the structure of the mature gingipain K catalytic domain plus IgSF domain. Kgp is the most active secreted proteolytic virulence factor of P. gingivalis and specifically celaves after lysines.

Carried out in the Proteolysis Lab in collaboration with the group of J. Potempa.

Tannerella forsythia prokarilysin

Tannerella forsythia prokarilysin catalytic domain (2015)

Despite being clearly an MMP according to sequence and structure, karilysin catalytic domain has a minimal pro-region juts spanning 14 residues.

Carried out in the Proteolysis Lab in collaboration with the group of J. Potempa.

Escherichia coli α2-macroglobulin ECAM (2015).

Extremely comprehesive study revealing the structural and functional basis of the action of this monomeric pan-endopeptidase inhibitor, which follows a snap-trap mechanism.

Carried out in the Proteolysis Lab in collaboration with S. Duquerroy and the group of J. Castón.    

Dionaea muscipula dionain

Dionaea muscipula dionain (2016).

Structure of the papain-type plant cysteine proteinase, dionain, from the carnivorous Venus flytrap (121).

Carried out in the Proteolysis Lab in collaboration with the group of J. Enghild.  

Bacillus anthracis immune inhibitor A1/2 (2016)

We performed the complete structure-function analysis of a metalloendopeptidase that is a modulator of the secretome of B. anthracis.

Carried out in the Proteolysis Lab in collaboration with the group of S. Leppla.  

C-terminal domain of Porphyromonas gingivalis RgpB (2016)

The type-IX secretion system of P. gingivalis. requires that the cargo proteins possess not just a specific peptide but rather a complete β-barrel domain.

Carried out in the Proteolysis Lab in collaboration with the group of J. Potempa and K.A. Nguyen.  

Porphyromonas gingivalis gingipain K pro-domain (2017)

We solved the structure of the ~200-residue pro-domain of gingipain K and could derive a novel mechanism of latency.

Carried out in the Proteolysis Lab in collaboration with the group of J. Potempa, I. Usón and J.A. Huntington.

Tannerella forsythia serine peptidase inhibitor miropin (2017)

We unveiled the mechanism of inhibition of serine and cysteine peptidases by this member of the serpin family of inhibitors.

Carried out in the Proteolysis Lab in collaboration with the group of J. Potempa.  

Porphyromonas gingivalis gingipain K in complex with the KYT-36 inhibitor (2019)

We solved the high-resolution (1.20 Å) complex structure of Kgp with KYT-36, a peptide-derived, potent, bioavailable and highly selective inhibitor, which is widely used for studies in vitro, in cells and in vivo .

Carried out in the Proteolysis Lab in collaboration with the group of J. Potempa.

Complex of mouse Fetuin-B in complex with crayfish Astacin (2019)

We determined the crystal structure of fetuin-B, unbound and in complex with archetypal astacin, and found that the inhibitor has tandem cystatin-type modules connected by an exposed linker with a rigid, disulfide-linked “CPDCP-trunk” and followed by an C-terminal region with little regular secondary structure. The CPDCP-trunk and a hairpin form a bipartite wedge, which slots into the active-site cleft of the MP.

Carried out in the Proteolysis Lab in collaboration with the groups of W. Jahnen-Dechent, L. Jovine and W. Stöcker.

Logo IBMB_csic-01

Logo CSIC

Logotipo_del_Ministerio_de_Economía_y_Competitividad

Generalitat

XRB

Feder-01