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PDBsum entry 1iad

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protein links
Zinc endopeptidase PDB id
1iad
Jmol
Contents
Protein chain
200 a.a. *
Waters ×172
* Residue conservation analysis
PDB id:
1iad
Name: Zinc endopeptidase
Title: Refined 1.8 angstroms x-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish astacus astacus l. Structure determination, refinement, molecular structure and comparison to thermolysin
Structure: Astacin. Chain: a. Engineered: yes
Source: Astacus astacus. Broad-fingered crayfish. Organism_taxid: 6715
Resolution:
2.30Å     R-factor:   0.155    
Authors: F.-X.Gomis-Rueth,W.Stoecker,W.Bode
Key ref: F.X.Gomis-Rüth et al. (1993). Refined 1.8 A X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. Structure determination, refinement, molecular structure and comparison with thermolysin. J Mol Biol, 229, 945-968. PubMed id: 8445658
Date:
09-May-94     Release date:   31-Aug-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07584  (ASTA_ASTFL) -  Astacin
Seq:
Struc:
251 a.a.
200 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.24.21  - Astacin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of peptide bonds in substrates containing five or more amino acids, preferentially with Ala in P1', and Pro in P2'.
      Cofactor: Zinc
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metallopeptidase activity     3 terms  

 

 
J Mol Biol 229:945-968 (1993)
PubMed id: 8445658  
 
 
Refined 1.8 A 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.
 
  ABSTRACT  
 
Astacin, a 200 residue digestive zinc-endopeptidase from the crayfish Astacus astacus L., is the prototype of the "astacin family", which comprises several membrane-bound mammalian endopeptidases and developmentally implicated regulatory proteins. Large trigonal crystals of astacin were grown, and X-ray reflection data to 1.8 A resolution were collected. The astacin structure has been solved by multiple isomorphous replacement using six heavy-atom derivatives, and refined to a crystallographic R-value of 0.158 applying stringent constraints. All 200 residues are clearly defined by electron density; 181 solvent molecules have been localized. Besides the native structure, the structures of Hg-astacin (with a mercury ion replacing the zinc) and of the apoenzyme were also refined. The astacin molecule exhibits a kidney-like shape. It consists of an amino-terminal and a carboxy-terminal domain, with a deep active-site cleft in between. The zinc ion, located at the bottom of this cleft, is co-ordinated in a novel trigonal-bipyramidal geometry by three histidine residues, a tyrosine and by a water molecule, which is also bound to the carboxylate side-chain of Glu93. The amino-terminal domain of astacin consists mainly of two long alpha-helices, one centrally located and one more peripheral, and of a five-stranded pleated beta-sheet. The amino terminus protrudes into an internal, water-filled cavity of the lower domain and forms a buried salt bridge with Glu103; amino-terminally extended pro-forms of astacin are thus not compatible with this structure. The carboxy-terminal domain of astacin is mainly organized in several turns and irregular structures. Because they share sequence identity of about 35%, the structures of the proteolytic domains of the other "astacin" members must be quite similar to astacin. Only a few very short deletions and insertions quite distant from the active-site distinguish their structures from astacin. The five-stranded beta-sheet and the two helices of the amino-terminal domain of astacin are topologically similar to the structure observed in the archetypal zinc-endopeptidase thermolysin; the rest of the structures are, in contrast, completely unrelated in astacin and thermolysin. The zinc ion, the central alpha-helix and the zinc-liganding residues His92, Glu93 and His96 of astacin are nearly superimposable with the respective groups of thermolysin, namely with the zinc ion, the "active-site helix", and His142TL, Glu143TL and His146TL of the zinc-binding consensus motif His-Glu-Xaa-Xaa-His (where Xaa is any amino acid residue).(ABSTRACT TRUNCATED AT 400 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18830233 P.Stańczak, J.Witecka, A.Szydło, E.Gutmajster, M.Lisik, A.Auguściak-Duma, M.Tarnowski, T.Czekaj, H.Czekaj, and A.L.Sieroń (2009).
Mutations in mammalian tolloid-like 1 gene detected in adult patients with ASD.
  Eur J Hum Genet, 17, 344-351.  
16509900 F.Möhrlen, M.Maniura, G.Plickert, M.Frohme, and U.Frank (2006).
Evolution of astacin-like metalloproteases in animals and their function in development.
  Evol Dev, 8, 223-231.  
16492671 G.F.da Silva, R.L.Reuille, L.J.Ming, and B.T.Livingston (2006).
Overexpression and mechanistic characterization of blastula protease 10, a metalloprotease involved in sea urchin embryogenesis and development.
  J Biol Chem, 281, 10737-10744.  
14709555 P.L.Tsai, C.H.Chen, C.J.Huang, C.M.Chou, and G.D.Chang (2004).
Purification and cloning of an endogenous protein inhibitor of carp nephrosin, an astacin metalloproteinase.
  J Biol Chem, 279, 11146-11155.  
14653817 F.Möhrlen, H.Hutter, and R.Zwilling (2003).
The astacin protein family in Caenorhabditis elegans.
  Eur J Biochem, 270, 4909-4920.  
12837794 S.Ravaud, P.Gouet, R.Haser, and N.Aghajari (2003).
Probing the role of divalent metal ions in a bacterial psychrophilic metalloprotease: binding studies of an enzyme in the crystalline state by x-ray crystallography.
  J Bacteriol, 185, 4195-4203.
PDB codes: 1o0q 1o0t 1om6 1om7 1om8 1omj
11815614 K.Kosowska, J.Reinholdt, L.K.Rasmussen, A.Sabat, J.Potempa, M.Kilian, and K.Poulsen (2002).
The Clostridium ramosum IgA proteinase represents a novel type of metalloendopeptidase.
  J Biol Chem, 277, 11987-11994.  
12034745 M.Heitzer, and A.Hallmann (2002).
An extracellular matrix-localized metalloproteinase with an exceptional QEXXH metal binding site prefers copper for catalytic activity.
  J Biol Chem, 277, 28280-28286.  
11322872 F.Möhrlen, S.Baus, A.Gruber, H.R.Rackwitz, M.Schnölzer, G.Vogt, and R.Zwilling (2001).
Activation of pro-astacin. Immunological and model peptide studies on the processing of immature astacin, a zinc-endopeptidase from the crayfish Astacus astacus.
  Eur J Biochem, 268, 2540-2546.  
11148046 J.E.Jackman, C.R.Raetz, and C.A.Fierke (2001).
Site-directed mutagenesis of the bacterial metalloamidase UDP-(3-O-acyl)-N-acetylglucosamine deacetylase (LpxC). Identification of the zinc binding site.
  Biochemistry, 40, 514-523.  
10813818 C.Marie-Claire, G.Tiraboschi, E.Ruffet, N.Inguimbert, M.C.Fournie-Zaluski, and B.P.Roques (2000).
Exploration of the S(')(1) subsite of neprilysin: a joined molecular modeling and site-directed mutagenesis study.
  Proteins, 39, 365-371.  
11053848 L.Bernardi, G.Vitale, C.Montecucco, and A.Musacchio (2000).
Expression, crystallization and preliminary X-ray diffraction studies of recombinant Bacillus anthracis lethal factor.
  Acta Crystallogr D Biol Crystallogr, 56, 1449-1451.  
10531480 X.Zhu, M.Teng, and L.Niu (1999).
Structure of acutolysin-C, a haemorrhagic toxin from the venom of Agkistrodon acutus, providing further evidence for the mechanism of the pH-dependent proteolytic reaction of zinc metalloproteinases.
  Acta Crystallogr D Biol Crystallogr, 55, 1834-1841.
PDB code: 1qua
9013553 B.X.Yan, and Y.Q.Sun (1997).
Glycine residues provide flexibility for enzyme active sites.
  J Biol Chem, 272, 3190-3194.  
  9385650 V.Villeret, J.P.Chessa, C.Gerday, and J.Van Beeumen (1997).
Preliminary crystal structure determination of the alkaline protease from the Antarctic psychrophile Pseudomonas aeruginosa.
  Protein Sci, 6, 2462-2464.  
8939981 A.Chestukhin, K.Muradov, L.Litovchick, and S.Shaltiel (1996).
The cleavage of protein kinase A by the kinase-splitting membranal proteinase is reproduced by meprin beta.
  J Biol Chem, 271, 30272-30280.  
8756323 F.Grams, V.Dive, A.Yiotakis, I.Yiallouros, S.Vassiliou, R.Zwilling, W.Bode, and W.Stöcker (1996).
Structure of astacin with a transition-state analogue inhibitor.
  Nat Struct Biol, 3, 671-675.
PDB codes: 1qji 1qjj
8706676 G.Lhomond, C.Ghiglione, T.Lepage, and C.Gache (1996).
Structure of the gene encoding the sea urchin blastula protease 10 (BP10), a member of the astacin family of Zn2+-metalloproteases.
  Eur J Biochem, 238, 744-751.  
7622493 A.Beaumont, M.J.O'Donohue, N.Paredes, N.Rousselet, M.Assicot, C.Bohuon, M.C.Fournié-Zaluski, and B.P.Roques (1995).
The role of histidine 231 in thermolysin-like enzymes. A site-directed mutagenesis study.
  J Biol Chem, 270, 16803-16808.  
  8536976 A.L.Finelli, T.Xie, C.A.Bossie, R.K.Blackman, and R.W.Padgett (1995).
The tolkin gene is a tolloid/BMP-1 homologue that is essential for Drosophila development.
  Genetics, 141, 271-281.  
8561847 D.Soler, T.Nomizu, W.E.Brown, Y.Shibata, and D.S.Auld (1995).
Matrilysin: expression, purification, and characterization.
  J Protein Chem, 14, 511-520.  
7737183 F.Grams, P.Reinemer, J.C.Powers, T.Kleine, M.Pieper, H.Tschesche, R.Huber, and W.Bode (1995).
X-ray structures of human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design.
  Eur J Biochem, 228, 830-841.
PDB codes: 1jao 1jaq
  7883008 H.Ostolaza, A.Soloaga, and F.M.Goñi (1995).
The binding of divalent cations to Escherichia coli alpha-haemolysin.
  Eur J Biochem, 228, 39-44.  
  7663339 W.Stöcker, F.Grams, U.Baumann, P.Reinemer, F.X.Gomis-Rüth, D.B.McKay, and W.Bode (1995).
The metzincins--topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases.
  Protein Sci, 4, 823-840.  
7583637 W.Stöcker, and W.Bode (1995).
Structural features of a superfamily of zinc-endopeptidases: the metzincins.
  Curr Opin Struct Biol, 5, 383-390.  
8078901 D.Zhang, I.Botos, F.X.Gomis-Rüth, R.Doll, C.Blood, F.G.Njoroge, J.W.Fox, W.Bode, and E.F.Meyer (1994).
Structural interaction of natural and synthetic inhibitors with the venom metalloproteinase, atrolysin C (form d).
  Proc Natl Acad Sci U S A, 91, 8447-8451.
PDB codes: 1atl 1htd
8053949 M.P.Vincenti, I.M.Clark, and C.E.Brinckerhoff (1994).
Using inhibitors of metalloproteinases to treat arthritis. Easier said than done?
  Arthritis Rheum, 37, 1115-1126.  
7656013 N.Borkakoti, F.K.Winkler, D.H.Williams, A.D'Arcy, M.J.Broadhurst, P.A.Brown, W.H.Johnson, and E.J.Murray (1994).
Structure of the catalytic domain of human fibroblast collagenase complexed with an inhibitor.
  Nat Struct Biol, 1, 106-110.
PDB code: 2tcl
7656014 P.R.Gooley, J.F.O'Connell, A.I.Marcy, G.C.Cuca, S.P.Salowe, B.L.Bush, J.D.Hermes, C.K.Esser, W.K.Hagmann, and J.P.Springer (1994).
The NMR structure of the inhibited catalytic domain of human stromelysin-1.
  Nat Struct Biol, 1, 111-118.
PDB codes: 1srt 2srt
  8137810 W.Bode, P.Reinemer, R.Huber, T.Kleine, S.Schnierer, and H.Tschesche (1994).
The X-ray crystal structure of the catalytic domain of human neutrophil collagenase inhibited by a substrate analogue reveals the essentials for catalysis and specificity.
  EMBO J, 13, 1263-1269.
PDB code: 1jap
  8223430 F.X.Gomis-Rüth, L.F.Kress, and W.Bode (1993).
First structure of a snake venom metalloproteinase: a prototype for matrix metalloproteinases/collagenases.
  EMBO J, 12, 4151-4157.
PDB code: 1iag
8248170 T.G.Wolfsberg, J.F.Bazan, C.P.Blobel, D.G.Myles, P.Primakoff, and J.M.White (1993).
The precursor region of a protein active in sperm-egg fusion contains a metalloprotease and a disintegrin domain: structural, functional, and evolutionary implications.
  Proc Natl Acad Sci U S A, 90, 10783-10787.  
  8253063 U.Baumann, S.Wu, K.M.Flaherty, and D.B.McKay (1993).
Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif.
  EMBO J, 12, 3357-3364.
PDB code: 1kap
8508794 W.Stöcker, F.X.Gomis-Rüth, W.Bode, and R.Zwilling (1993).
Implications of the three-dimensional structure of astacin for the structure and function of the astacin family of zinc-endopeptidases.
  Eur J Biochem, 214, 215-231.
PDB code: 1iaf
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