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PDBsum entry 1vz8

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1vz8
Jmol
Contents
Protein chains
376 a.a. *
Ligands
SO4 ×6
Waters ×43
* Residue conservation analysis
PDB id:
1vz8
Name: Transferase
Title: Ornithine acetyltransferase (orf6 gene product - clavulanic acid biosynthesis) from streptomyces clavuligerus (semet structure)
Structure: Ornithine acetyl-transferase. Chain: a, b, c, d. Engineered: yes. Other_details: selenomethionine-substituted
Source: Streptomyces clavuligerus. Organism_taxid: 1901. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.75Å     R-factor:   0.235     R-free:   0.288
Authors: J.M.Elkins,N.J.Kershaw,C.J.Schofield
Key ref: J.M.Elkins et al. (2005). X-ray crystal structure of ornithine acetyltransferase from the clavulanic acid biosynthesis gene cluster. Biochem J, 385, 565-573. PubMed id: 15352873 DOI: 10.1042/BJ20040814
Date:
14-May-04     Release date:   16-Sep-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam  
P0DJQ5  (GNAT2_STRCL) -  Glutamate N-acetyltransferase 2
Seq:
Struc:
393 a.a.
376 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.35  - Glutamate N-acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: N2-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L- glutamate
N(2)-acetyl-L-ornithine
+ L-glutamate
= L-ornithine
+ N-acetyl-L- glutamate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     clavulanic acid biosynthetic process   2 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1042/BJ20040814 Biochem J 385:565-573 (2005)
PubMed id: 15352873  
 
 
X-ray crystal structure of ornithine acetyltransferase from the clavulanic acid biosynthesis gene cluster.
J.M.Elkins, N.J.Kershaw, C.J.Schofield.
 
  ABSTRACT  
 
The orf6 gene from the clavulanic acid biosynthesis gene cluster encodes an OAT (ornithine acetyltransferase). Similar to other OATs the enzyme has been shown to catalyse the reversible transfer of an acetyl group from N-acetylornithine to glutamate. OATs are Ntn (N-terminal nucleophile) enzymes, but are distinct from the better-characterized Ntn hydrolase enzymes as they catalyse acetyl transfer rather than a hydrolysis reaction. In the present study, we describe the X-ray crystal structure of the OAT, corresponding to the orf6 gene product, to 2.8 A (1 A=0.1 nm) resolution. The larger domain of the structure consists of an alphabetabetaalpha sandwich as in the structures of Ntn hydrolase enzymes. However, differences in the connectivity reveal that OATs belong to a structural family different from that of other structurally characterized Ntn enzymes, with one exception: unexpectedly, the alphabetabetaalpha sandwich of ORF6 (where ORF stands for open reading frame) displays the same fold as an DmpA (L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi), and so the OATs and DmpA form a new structural subfamily of Ntn enzymes. The structure reveals an alpha2beta2-heterotetrameric oligomerization state in which the intermolecular interface partly defines the active site. Models of the enzyme-substrate complexes suggest a probable oxyanion stabilization mechanism as well as providing insight into how the enzyme binds its two differently charged substrates.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19194014 R.Sankaranarayanan, C.R.Garen, M.M.Cherney, M.Yuan, C.Lee, and M.N.James (2009).
Preliminary X-ray crystallographic analysis of ornithine acetyltransferase (Rv1653) from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 173-176.  
17318535 B.Geueke, and H.P.Kohler (2007).
Bacterial beta-peptidyl aminopeptidases: on the hydrolytic degradation of beta-peptides.
  Appl Microbiol Biotechnol, 74, 1197-1204.  
17347518 Y.Xu, B.Labedan, and N.Glansdorff (2007).
Surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms.
  Microbiol Mol Biol Rev, 71, 36-47.  
  17142921 D.Maes, M.Crabeel, C.Van de Weerdt, J.Martial, E.Peeters, D.Charlier, K.Decanniere, C.Vanhee, L.Wyns, and I.Zegers (2006).
Crystallization of ornithine acetyltransferase from yeast by counter-diffusion and preliminary X-ray study.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1294-1297.  
16251194 H.Arulanantham, N.J.Kershaw, K.S.Hewitson, C.E.Hughes, J.E.Thirkettle, and C.J.Schofield (2006).
ORF17 from the clavulanic acid biosynthesis gene cluster catalyzes the ATP-dependent formation of N-glycyl-clavaminic acid.
  J Biol Chem, 281, 279-287.  
15937278 H.Cheng, and N.V.Grishin (2005).
DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.
  Protein Sci, 14, 1902-1910.  
15946951 K.Michalska, K.Brzezinski, and M.Jaskolski (2005).
Crystal structure of isoaspartyl aminopeptidase in complex with L-aspartate.
  J Biol Chem, 280, 28484-28491.
PDB codes: 1seo 2zal
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