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PDBsum entry 1azz
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protein Protein-protein interface(s) links
Complex (serine protease/inhibitor) PDB id
1azz

 

 

 

 

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Contents
Protein chains
226 a.a. *
137 a.a. *
Waters ×140
* Residue conservation analysis
PDB id:
1azz
Name: Complex (serine protease/inhibitor)
Title: Fiddler crab collagenase complexed to ecotin
Structure: Collagenase. Chain: a, b. Ecotin. Chain: c, d. Synonym: trypsin inhibitor
Source: Celuca pugilator. Atlantic sand fiddler crab. Organism_taxid: 6772. Other_details: crab hepatopancreas. Escherichia coli. Organism_taxid: 562. Plasmid: ptactac
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.189     R-free:   0.238
Authors: J.J.Perona,R.J.Fletterick
Key ref:
J.J.Perona et al. (1997). Crystal structure of an ecotin-collagenase complex suggests a model for recognition and cleavage of the collagen triple helix. Biochemistry, 36, 5381-5392. PubMed id: 9154920 DOI: 10.1021/bi9617522
Date:
24-Nov-97     Release date:   25-Feb-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00771  (COGS_LEPPG) -  Brachyurin from Leptuca pugilator
Seq:
Struc: 		226 a.a.
226 a.a.
Protein chains
Pfam   ArchSchema ?
P23827  (ECOT_ECOLI) -  Ecotin from Escherichia coli (strain K12)
Seq:
Struc: 		162 a.a.
137 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.4.21.32  - brachyurin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins, with broad specificity for peptide bonds. Degrades native collagen at about 75% of the length of the molecule from the N-terminus. Low activity on small molecule substrates of both trypsin and chymotrypsin.

 

 
DOI no: 10.1021/bi9617522 Biochemistry 36:5381-5392 (1997)
PubMed id: 9154920  
 
 
Crystal structure of an ecotin-collagenase complex suggests a model for recognition and cleavage of the collagen triple helix.
J.J.Perona, C.A.Tsu, C.S.Craik, R.J.Fletterick.
 
  ABSTRACT  
 
The crystal structure of fiddler crab collagenase complexed with the dimeric serine protease inhibitor ecotin at 2.5 A resolution reveals an extended cleft providing binding sites for at least 11 contiguous substrate residues. Comparison of the positions of nine intermolecular main chain hydrogen bonding interactions in the cleft, with the known sequences at the cleavage site of type I collagen, suggests that the protease binding loop of ecotin adopts a conformation mimicking that of the cleaved strand of collagen. A well-defined groove extending across the binding surface of the enzyme readily accommodates the two other polypeptide chains of the triple-helical substrate. These observations permit construction of a detailed molecular model for collagen recognition and cleavage by this invertebrate serine protease. Ecotin undergoes a pronounced internal structural rearrangement which permits binding in the observed conformation. The capacity for such rearrangement appears to be a key determinant of its ability to inhibit a wide range of serine proteases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21418586 E.Mancini, F.Tammaro, F.Baldini, A.Via, D.Raimondo, P.George, P.Audisio, I.V.Sharakhov, A.Tramontano, F.Catteruccia, and A.della Torre (2011).
Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract.
  BMC Evol Biol, 11, 72.  
20180651 A.A.Stoop, R.V.Joshi, C.T.Eggers, and C.S.Craik (2010).
Analysis of an engineered plasma kallikrein inhibitor and its effect on contact activation.
  Biol Chem, 391, 425-433.  
20649906 E.Perera, T.Pons, D.Hernandez, F.J.Moyano, G.Martínez-Rodríguez, and J.M.Mancera (2010).
New members of the brachyurins family in lobster include a trypsin-like enzyme with amino acid substitutions in the substrate-binding pocket.
  FEBS J, 277, 3489-3501.  
19698094 C.Fufezan, and M.Specht (2009).
p3d--Python module for structural bioinformatics.
  BMC Bioinformatics, 10, 258.  
18695720 A.I.Papisova, S.A.Semenova, I.u.A.Kislitsyn, and G.N.Rudenskaia (2008).
[Characteristics of substrate hydrolysis by endopeptidases from the hepatopancreas of the king crab]
  Bioorg Khim, 34, 479-486.  
16843700 H.C.Castro, R.Q.Monteiro, M.Assafim, N.I.Loureiro, C.Craik, and R.B.Zingali (2006).
Ecotin modulates thrombin activity through exosite-2 interactions.
  Int J Biochem Cell Biol, 38, 1893-1900.  
15759084 A.Gudmundsdóttir, and H.M.Pálsdóttir (2005).
Atlantic cod trypsins: from basic research to practical applications.
  Mar Biotechnol (NY), 7, 77-88.  
16237016 E.Matsuda, N.Abe, H.Tamakawa, J.Kaneko, and Y.Kamio (2005).
Gene cloning and molecular characterization of an extracellular poly(L-lactic acid) depolymerase from Amycolatopsis sp. strain K104-1.
  J Bacteriol, 187, 7333-7340.  
15545266 L.Jin, P.Pandey, R.E.Babine, J.C.Gorga, K.J.Seidl, E.Gelfand, D.T.Weaver, S.S.Abdel-Meguid, and J.E.Strickler (2005).
Crystal structures of the FXIa catalytic domain in complex with ecotin mutants reveal substrate-like interactions.
  J Biol Chem, 280, 4704-4712.
PDB codes: 1xx9 1xxd 1xxf
15014068 A.Wlodawer, M.Li, A.Gustchina, N.Tsuruoka, M.Ashida, H.Minakata, H.Oyama, K.Oda, T.Nishino, and T.Nakayama (2004).
Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity.
  J Biol Chem, 279, 21500-21510.
PDB codes: 1sio 1siu 1sn7
15123647 S.W.Ruggles, R.J.Fletterick, and C.S.Craik (2004).
Characterization of structural determinants of granzyme B reveals potent mediators of extended substrate specificity.
  J Biol Chem, 279, 30751-30759.  
12682007 J.J.Wilson, O.Matsushita, A.Okabe, and J.Sakon (2003).
A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation.
  EMBO J, 22, 1743-1752.
PDB codes: 1nqd 1nqj
12819769 J.K.Bell, D.H.Goetz, S.Mahrus, J.L.Harris, R.J.Fletterick, and C.S.Craik (2003).
The oligomeric structure of human granzyme A is a determinant of its extended substrate specificity.
  Nat Struct Biol, 10, 527-534.
PDB code: 1orf
12437096 A.Gudmundsdóttir (2002).
Cold-adapted and mesophilic brachyurins.
  Biol Chem, 383, 1125-1131.  
12228918 J.L.Lauer-Fields, D.Juska, and G.B.Fields (2002).
Matrix metalloproteinases and collagen catabolism.
  Biopolymers, 66, 19-32.  
12437092 J.L.Lauer-Fields, and G.B.Fields (2002).
Triple-helical peptide analysis of collagenolytic protease activity.
  Biol Chem, 383, 1095-1105.  
11733020 A.Bódi, G.Kaslik, I.Venekei, and L.Gráf (2001).
Structural determinants of the half-life and cleavage site preference in the autolytic inactivation of chymotrypsin.
  Eur J Biochem, 268, 6238-6246.  
11121112 D.C.Benjamin, S.Kristjánsdóttir, and A.Gudmundsdóttir (2001).
Increasing the thermal stability of euphauserase. A cold-active and multifunctional serine protease from Antarctic krill.
  Eur J Biochem, 268, 127-131.  
11468352 M.D.Person, K.C.Brown, S.Mahrus, C.S.Craik, and A.L.Burlingame (2001).
Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer.
  Protein Sci, 10, 1549-1562.  
10673425 C.C.Deivanayagam, R.L.Rich, M.Carson, R.T.Owens, S.Danthuluri, T.Bice, M.Höök, and S.V.Narayana (2000).
Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein.
  Structure, 8, 67-78.
PDB codes: 1d2o 1d2p
10852705 C.Luke, C.Schick, C.Tsu, J.C.Whisstock, J.A.Irving, D.Brömme, L.Juliano, G.P.Shi, H.A.Chapman, and G.A.Silverman (2000).
Simple modifications of the serpin reactive site loop convert SCCA2 into a cysteine proteinase inhibitor: a critical role for the P3' proline in facilitating RSL cleavage.
  Biochemistry, 39, 7081-7091.  
10713532 I.Broutin-L'Hermite, M.Ries-Kautt, and A.Ducruix (2000).
1.7 A x-ray structure of space-grown collagenase crystals.
  Acta Crystallogr D Biol Crystallogr, 56, 376-378.  
10785384 S.Kristjánsdóttir, and A.Gudmundsdóttir (2000).
Propeptide dependent activation of the Antarctic krill euphauserase precursor produced in yeast.
  Eur J Biochem, 267, 2632-2639.  
10216315 C.S.Lee, I.S.Seong, H.K.Song, C.H.Chung, and S.W.Suh (1999).
Crystallization and preliminary X-ray crystallographic analysis of the protease inhibitor ecotin in complex with chymotrypsin.
  Acta Crystallogr D Biol Crystallogr, 55, 1091-1092.  
10102985 H.Czapinska, and J.Otlewski (1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
  Eur J Biochem, 260, 571-595.  
10455165 R.L.Rich, C.C.Deivanayagam, R.T.Owens, M.Carson, A.Höök, D.Moore, J.Symersky, V.W.Yang, S.V.Narayana, and M.Höök (1999).
Trench-shaped binding sites promote multiple classes of interactions between collagen and the adherence receptors, alpha(1)beta(1) integrin and Staphylococcus aureus cna MSCRAMM.
  J Biol Chem, 274, 24906-24913.
PDB code: 1qc5
10318785 S.Réhault, M.Brillard-Bourdet, M.A.Juliano, L.Juliano, F.Gauthier, and T.Moreau (1999).
New, sensitive fluorogenic substrates for human cathepsin G based on the sequence of serpin-reactive site loops.
  J Biol Chem, 274, 13810-13817.  
9675278 J.Polanowska, I.Krokoszynska, H.Czapinska, W.Watorek, M.Dadlez, and J.Otlewski (1998).
Specificity of human cathepsin G.
  Biochim Biophys Acta, 1386, 189-198.  
9521759 K.C.Brown, Z.Yu, A.L.Burlingame, and C.S.Craik (1998).
Determining protein-protein interactions by oxidative cross-linking of a glycine-glycine-histidine fusion protein.
  Biochemistry, 37, 4397-4406.  
9799504 R.L.Rich, B.Demeler, K.Ashby, C.C.Deivanayagam, J.W.Petrich, J.M.Patti, S.V.Narayana, and M.Höök (1998).
Domain structure of the Staphylococcus aureus collagen adhesin.
  Biochemistry, 37, 15423-15433.  
9154921 C.A.Tsu, J.J.Perona, R.J.Fletterick, and C.S.Craik (1997).
Structural basis for the broad substrate specificity of fiddler crab collagenolytic serine protease 1.
  Biochemistry, 36, 5393-5401.  
9374470 J.J.Perona, and C.S.Craik (1997).
Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold.
  J Biol Chem, 272, 29987-29990.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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