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PDBsum entry 1iae

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Zinc endopeptidase PDB id
1iae
Jmol
Contents
Protein chain
200 a.a. *
Metals
_NI
Waters ×184
* Residue conservation analysis
PDB id:
1iae
Name: Zinc endopeptidase
Title: 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 activity
Structure: Astacin. Chain: a. Engineered: yes
Source: Astacus astacus. Broad-fingered crayfish. Organism_taxid: 6715
Resolution:
1.83Å     R-factor:   0.143    
Authors: F.Grams,W.Stoecker,W.Bode
Key ref: F.X.Gomis-Rüth et al. (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 activity. J Biol Chem, 269, 17111-17117. PubMed id: 8006015
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: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metallopeptidase activity     3 terms  

 

 
J Biol Chem 269:17111-17117 (1994)
PubMed id: 8006015  
 
 
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 activity.
F.X.Gomis-Rüth, F.Grams, I.Yiallouros, H.Nar, U.Küsthardt, R.Zwilling, W.Bode, W.Stöcker.
 
  ABSTRACT  
 
The catalytic zinc ion of astacin, a prototypical metalloproteinase from crayfish, has been substituted by Co(II), Cu(II), Hg(II), and Ni(II) in order to probe the role of the metal for both catalysis and structure. Compared to Zn(II)-astacin, Co(II)- and Cu(II)-astacin display enzymatic activities of about 140 and 37%, respectively, while Ni(II)- and Hg(II)-astacin are almost inactive. The electron paramagnetic resonance spectrum of Cu(II)-astacin is typical of 5-fold coordinated copper(II), and its intense absorption maxima at 445 and 325 nm are probably due to ligand-metal charge-transfer transitions involving Tyr-149. This residue had been identified previously by x-ray crystallography of the zinc enzyme as a zinc ligand, in addition to three imidazoles and a glutamic acid-bound water molecule. We present now the refined high-resolution x-ray crystal structures of Cu(II)-, Co(II)-, and Ni(II)-astacin, which exhibit a virtually identical protein framework to the previously analyzed structures of Zn(II)-, apo-, and Hg(II)-astacin. In Co(II)- and Cu(II)-astacin, the metal is penta-coordinated similarly to the native zinc enzyme. In the Ni(II) derivative, however, an additional solvent molecule expands the metal coordination sphere to a distorted octahedral ligand geometry, while in Hg(II)-astacin, no ordered solvent molecule at all is observed in the inner coordination sphere of the metal. This indicates a close correlation between catalytic properties and ground-state metal coordination of astacin.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20544098 M.Qaiser Fatmi, T.S.Hofer, and B.M.Rode (2010).
The stability of [Zn(NH(3))(4)](2+) in water: A quantum mechanical/molecular mechanical molecular dynamics study.
  Phys Chem Chem Phys, 12, 9713-9718.  
20333422 O.E.Johnson, K.C.Ryan, M.J.Maroney, and T.C.Brunold (2010).
Spectroscopic and computational investigation of three Cys-to-Ser mutants of nickel superoxide dismutase: insight into the roles played by the Cys2 and Cys6 active-site residues.
  J Biol Inorg Chem, 15, 777-793.  
15792365 K.Peters, H.Schmidt, R.E.Unger, G.Kamp, F.Pröls, B.J.Berger, and C.J.Kirkpatrick (2005).
Paradoxical effects of hypoxia-mimicking divalent cobalt ions in human endothelial cells in vitro.
  Mol Cell Biochem, 270, 157-166.  
9665723 E.G.Orellano, J.E.Girardini, J.A.Cricco, E.A.Ceccarelli, and A.J.Vila (1998).
Spectroscopic characterization of a binuclear metal site in Bacillus cereus beta-lactamase II.
  Biochemistry, 37, 10173-10180.  
9628737 S.L.Clugston, J.F.Barnard, R.Kinach, D.Miedema, R.Ruman, E.Daub, and J.F.Honek (1998).
Overproduction and characterization of a dimeric non-zinc glyoxalase I from Escherichia coli: evidence for optimal activation by nickel ions.
  Biochemistry, 37, 8754-8763.  
9275172 R.Balakrishnan, N.Ramasubbu, K.I.Varughese, and R.Parthasarathy (1997).
Crystal structures of the copper and nickel complexes of RNase A: metal-induced interprotein interactions and identification of a novel copper binding motif.
  Proc Natl Acad Sci U S A, 94, 9620-9625.
PDB code: 1aqp
8643539 S.W.Li, A.L.Sieron, A.Fertala, Y.Hojima, W.V.Arnold, and D.J.Prockop (1996).
The C-proteinase that processes procollagens to fibrillar collagens is identical to the protein previously identified as bone morphogenic protein-1.
  Proc Natl Acad Sci U S A, 93, 5127-5130.  
  7670368 J.S.Bond, and R.J.Beynon (1995).
The astacin family of metalloendopeptidases.
  Protein Sci, 4, 1247-1261.  
  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.  
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