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PDBsum entry 1obr

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protein ligands metals links
Hydrolase PDB id
1obr
Jmol
Contents
Protein chain
323 a.a. *
Ligands
SO4
Metals
_ZN
_CA ×4
Waters ×118
* Residue conservation analysis
PDB id:
1obr
Name: Hydrolase
Title: Carboxypeptidase t
Structure: Carboxypeptidase t. Chain: a. Ec: 3.4.17.18
Source: Thermoactinomyces vulgaris. Organism_taxid: 2026
Biol. unit: Monomer (from PDB file)
Resolution:
2.30Å     R-factor:   0.152    
Authors: A.Teplyakov,K.Polyakov,G.Obmolova,A.Osterman
Key ref: A.Teplyakov et al. (1992). Crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris. Eur J Biochem, 208, 281-288. PubMed id: 1521526
Date:
22-Jun-96     Release date:   11-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29068  (CBPT_THEVU) -  Carboxypeptidase T
Seq:
Struc:
424 a.a.
323 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.17.18  - Carboxypeptidase T.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of a C-terminal residue, which may be hydrophobic or positively charged.
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     zinc ion binding     2 terms  

 

 
Eur J Biochem 208:281-288 (1992)
PubMed id: 1521526  
 
 
Crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris.
A.Teplyakov, K.Polyakov, G.Obmolova, B.Strokopytov, I.Kuranova, A.Osterman, N.Grishin, S.Smulevitch, O.Zagnitko, O.Galperina.
 
  ABSTRACT  
 
The crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris has been determined at 0.235-nm resolution by X-ray diffraction. Carboxypeptidase T is a remote homologue of mammalian Zn-carboxypeptidases. In spite of the low degree of amino acid sequence identity, the three-dimensional structure of carboxypeptidase T is very similar to that of pancreatic carboxypeptidases A and B. The core of the protein molecule is formed by an eight-stranded mixed beta sheet. The active site is located at the C-edge of the central (parallel) part of the beta sheet. The structural organization of the active centre appears to be essentially the same in the three carboxypeptidases. Amino acid residues directly involved in catalysis and binding of the C-terminal carboxyl of a substrate are strictly conserved. This suggests that the catalytic mechanism proposed for the pancreatic enzymes is applicable to carboxypeptidase T and to the whole family of Zn-carboxypeptidases. Comparison of the amino acid replacements at the primary specificity pocket of carboxypeptidases A, B and T provides an explanation of the unusual 'A+B' type of specificity of carboxypeptidase T. Four calcium-binding sites localized in the crystal structure of carboxypeptidase T could account for the high thermostability of the protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18991561 A.M.Grishin, V.K.h.Akparov, and G.G.Chestukhina (2008).
Leu254 residue and calcium ions as new structural determinants of carboxypeptidase T substrate specificity.
  Biochemistry (Mosc), 73, 1140-1145.  
17888003 M.Firczuk, and M.Bochtler (2007).
Folds and activities of peptidoglycan amidases.
  FEMS Microbiol Rev, 31, 676-691.  
17511606 V.K.h.Akparov, A.M.Grishin, M.P.Yusupova, N.M.Ivanova, and G.G.Chestukhina (2007).
Structural principles of the wide substrate specificity of Thermoactinomyces vulgaris carboxypeptidase T. Reconstruction of the carboxypeptidase B primary specificity pocket.
  Biochemistry (Mosc), 72, 416-423.  
16617426 H.Deng, G.Chen, W.Yang, and J.J.Yang (2006).
Predicting calcium-binding sites in proteins - a graph theory and geometry approach.
  Proteins, 64, 34-42.  
14997549 I.Hudáky, Z.Gáspári, O.Carugo, M.Cemazar, S.Pongor, and A.Perczel (2004).
Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations.
  Proteins, 55, 152-168.  
12885660 E.Occhipinti, P.L.Martelli, F.Spinozzi, F.Corsi, C.Formantici, L.Molteni, H.Amenitsch, P.Mariani, P.Tortora, and R.Casadio (2003).
3D structure of Sulfolobus solfataricus carboxypeptidase developed by molecular modeling is confirmed by site-directed mutagenesis and small angle X-ray scattering.
  Biophys J, 85, 1165-1175.  
12724517 M.Cemazar, S.Zahariev, J.J.Lopez, O.Carugo, J.A.Jones, P.J.Hore, and S.Pongor (2003).
Oxidative folding intermediates with nonnative disulfide bridges between adjacent cysteine residues.
  Proc Natl Acad Sci U S A, 100, 5754-5759.  
12842879 Y.Yang, J.Poncet, J.Garnier, C.Zatylny, E.Bachère, and A.Aumelas (2003).
Solution structure of the recombinant penaeidin-3, a shrimp antimicrobial peptide.
  J Biol Chem, 278, 36859-36867.
PDB code: 1ueo
12111749 C.T.Supuran, A.Scozzafava, and B.W.Clare (2002).
Bacterial protease inhibitors.
  Med Res Rev, 22, 329-372.  
11157230 K.Ishikawa, H.Ishida, I.Matsui, Y.Kawarabayasi, and H.Kikuchi (2001).
Novel bifunctional hyperthermostable carboxypeptidase/aminoacylase from Pyrococcus horikoshii OT3.
  Appl Environ Microbiol, 67, 673-679.  
11292843 N.V.Grishin (2001).
Treble clef finger--a functionally diverse zinc-binding structural motif.
  Nucleic Acids Res, 29, 1703-1714.  
10545093 F.X.Gomis-Rüth, V.Companys, Y.Qian, L.D.Fricker, J.Vendrell, F.X.Avilés, and M.Coll (1999).
Crystal structure of avian carboxypeptidase D domain II: a prototype for the regulatory metallocarboxypeptidase subfamily.
  EMBO J, 18, 5817-5826.
PDB code: 1qmu
10073577 Y.Lei, X.Xin, D.Morgan, J.E.Pintar, and L.D.Fricker (1999).
Identification of mouse CPX-1, a novel member of the metallocarboxypeptidase gene family with highest similarity to CPX-2.
  DNA Cell Biol, 18, 175-185.  
9503606 A.M.Bushueva, A.B.Shevelev, J.Gumpert, G.G.Chestukhina, A.V.Serkina, C.Hoischen, M.V.Matz, M.V.Kuryatova, and V.M.Stepanov (1998).
Expression of the carboxypeptidase T gene from Thermoactinomyces vulgaris in stable protoplast type L-forms of Proteus mirabilis.
  FEMS Microbiol Lett, 159, 145-150.  
9083113 S.Rowsell, R.A.Pauptit, A.D.Tucker, R.G.Melton, D.M.Blow, and P.Brick (1997).
Crystal structure of carboxypeptidase G2, a bacterial enzyme with applications in cancer therapy.
  Structure, 5, 337-347.
PDB code: 1cg2
8662840 O.Varlamov, E.H.Leiter, and L.Fricker (1996).
Induced and spontaneous mutations at Ser202 of carboxypeptidase E. Effect on enzyme expression, activity, and intracellular routing.
  J Biol Chem, 271, 13981-13986.  
  7559343 S.Colombo, G.Toietta, L.Zecca, M.Vanoni, and P.Tortora (1995).
Molecular cloning, nucleotide sequence, and expression of a carboxypeptidase-encoding gene from the archaebacterium Sulfolobus solfataricus.
  J Bacteriol, 177, 5561-5566.  
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 code is shown on the right.