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PDBsum entry 1a0g

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1a0g
Jmol
Contents
Protein chains
280 a.a. *
Ligands
PMP ×2
Waters ×166
* Residue conservation analysis
PDB id:
1a0g
Name: Transferase
Title: L201a mutant of d-amino acid aminotransferase complexed with pyridoxamine-5'-phosphate
Structure: D-amino acid aminotransferase. Chain: a, b. Synonym: d-alanine aminotransferase, d-aspartate aminotrans engineered: yes. Mutation: yes. Other_details: pyridoxamine-5'-phosphates are non-covalentl the enzyme molecules
Source: Bacillus sp.. Organism_taxid: 72579. Strain: ym-1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.216     R-free:   0.263
Authors: S.Sugio,A.Kashima,K.Kishimoto,D.Peisach,G.A.Petsko,D.Ringe, T.Yoshimura,N.Esaki
Key ref: S.Sugio et al. (1998). Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination. Protein Eng, 11, 613-619. PubMed id: 9749913
Date:
30-Nov-97     Release date:   03-Jun-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19938  (DAAA_BACYM) -  D-alanine aminotransferase
Seq:
Struc:
283 a.a.
280 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.6.1.21  - D-amino-acid transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-alanine + 2-oxoglutarate = pyruvate + D-glutamate
D-alanine
+ 2-oxoglutarate
= pyruvate
+ D-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PMP) matches with 88.24% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
Protein Eng 11:613-619 (1998)
PubMed id: 9749913  
 
 
Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination.
S.Sugio, A.Kashima, K.Kishimoto, D.Peisach, G.A.Petsko, D.Ringe, T.Yoshimura, N.Esaki.
 
  ABSTRACT  
 
The leucine-to-alanine mutation at residue 201 of D-amino acid aminotransferase provides a unique enzyme which gradually loses its activity while catalyzing the normal transamination; the co-enzyme form is converted from pyridoxal 5'-phosphate to pyridoxamine 5'-phosphate upon the inactivation [Kishimoto,K., Yoshimura,T., Esaki,N., Sugio,S., Manning,J.M. and Soda,K. (1995) J. Biochem., 117, 691-696]. Crystal structures of both co-enzyme forms of the mutant enzyme have been determined at 2.0 A resolution: they are virtually identical, and are quite similar to that of the wild-type enzyme. Significant differences in both forms of the mutant are localized only on the bound co-enzyme, the side chains of Lys145 and Tyr31, and a water molecule sitting on the putative substrate binding site. Detailed comparisons of the structures of the mutant, together with that of the pyridoxamine-5'-phosphate form of the wild-type enzyme, imply that Leu201 would play a crucial role in the transamination reaction by keeping the pyridoxyl ring in the proper location without disturbing its oscillating motion, although the residue seems to not be especially important for the structural integrity of the enzyme.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18266853 H.Barreteau, A.Kovac, A.Boniface, M.Sova, S.Gobec, and D.Blanot (2008).
Cytoplasmic steps of peptidoglycan biosynthesis.
  FEMS Microbiol Rev, 32, 168-207.  
11264579 N.Yennawar, J.Dunbar, M.Conway, S.Hutson, and G.Farber (2001).
The structure of human mitochondrial branched-chain aminotransferase.
  Acta Crystallogr D Biol Crystallogr, 57, 506-515.
PDB codes: 1ekf 1ekp 1ekv
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