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PDBsum entry 1yaa

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protein ligands Protein-protein interface(s) links
Aminotransferase PDB id
1yaa
Jmol
Contents
Protein chains
412 a.a. *
Ligands
MAE ×4
PLP ×4
Waters ×716
* Residue conservation analysis
PDB id:
1yaa
Name: Aminotransferase
Title: Aspartate aminotransferase from saccharomyces cerevisiae cyt
Structure: Aspartate aminotransferase. Chain: a, b, c, d. Other_details: pyridoxal phosphate cofactor covalently boun 258 via schiff base linkage in each subunit
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Cellular_location: cytoplasm
Biol. unit: Dimer (from PDB file)
Resolution:
2.05Å     R-factor:   0.231     R-free:   0.299
Authors: C.J.Jeffery
Key ref: C.J.Jeffery et al. (1998). Crystal structure of Saccharomyces cerevisiae cytosolic aspartate aminotransferase. Protein Sci, 7, 1380-1387. PubMed id: 9655342 DOI: 10.1002/pro.5560070614
Date:
27-Jan-98     Release date:   16-Sep-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23542  (AATC_YEAST) -  Aspartate aminotransferase, cytoplasmic
Seq:
Struc:
418 a.a.
412 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.6.1.1  - Aspartate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
L-aspartate
Bound ligand (Het Group name = MAE)
matches with 88.89% similarity
+ 2-oxoglutarate
= oxaloacetate
+ L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     biosynthetic process   6 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1002/pro.5560070614 Protein Sci 7:1380-1387 (1998)
PubMed id: 9655342  
 
 
Crystal structure of Saccharomyces cerevisiae cytosolic aspartate aminotransferase.
C.J.Jeffery, T.Barry, S.Doonan, G.A.Petsko, D.Ringe.
 
  ABSTRACT  
 
The crystal structure of Saccharomyces cerevisiae cytoplasmic aspartate aminotransferase (EC 2.6.1.1) has been determined to 2.05 A resolution in the presence of the cofactor pyridoxal-5'-phosphate and the competitive inhibitor maleate. The structure was solved by the method of molecular replacement. The final value of the crystallographic R-factor after refinement was 23.1% with good geometry of the final model. The yeast cytoplasmic enzyme is a homodimer with two identical active sites containing residues from each subunit. It is found in the "closed" conformation with a bound maleate inhibitor in each active site. It shares the same three-dimensional fold and active site residues as the aspartate aminotransferases from Escherichia coli, chicken cytoplasm, and chicken mitochondria, although it shares less than 50% sequence identity with any of them. The availability of four similar enzyme structures from distant regions of the evolutionary tree provides a measure of tolerated changes that can arise during millions of years of evolution.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18922152 J.M.Thornburg, K.K.Nelson, B.F.Clem, A.N.Lane, S.Arumugam, A.Simmons, J.W.Eaton, S.Telang, and J.Chesney (2008).
Targeting aspartate aminotransferase in breast cancer.
  Breast Cancer Res, 10, R84.  
16894611 B.Popovic, X.Tang, D.Y.Chirgadze, F.Huang, T.L.Blundell, and J.B.Spencer (2006).
Crystal structures of the PLP- and PMP-bound forms of BtrR, a dual functional aminotransferase involved in butirosin biosynthesis.
  Proteins, 65, 220-230.
PDB codes: 2c7t 2c81
12595727 J.K.Yang, C.Chang, S.J.Cho, J.Y.Lee, Y.G.Yu, S.H.Eom, and S.W.Suh (2003).
Crystallization and preliminary X-ray analysis of the Mj0684 gene product, a putative aspartate aminotransferase, from Methanococcus jannaschii.
  Acta Crystallogr D Biol Crystallogr, 59, 563-565.  
11967363 E.Deu, K.A.Koch, and J.F.Kirsch (2002).
The role of the conserved Lys68*:Glu265 intersubunit salt bridge in aspartate aminotransferase kinetics: multiple forced covariant amino acid substitutions in natural variants.
  Protein Sci, 11, 1062-1073.  
11443076 L.C.Berger, J.Wilson, P.Wood, and B.J.Berger (2001).
Methionine regeneration and aspartate aminotransferase in parasitic protozoa.
  J Bacteriol, 183, 4421-4434.  
10673430 G.Schneider, H.Käck, and Y.Lindqvist (2000).
The manifold of vitamin B6 dependent enzymes.
  Structure, 8, R1-R6.  
10584065 A.Poupon, F.Jebai, G.Labesse, F.Gros, J.Thibault, J.P.Mornon, and M.Krieger (1999).
Structure modelling and site-directed mutagenesis of the rat aromatic L-amino acid pyridoxal 5'-phosphate-dependent decarboxylase: a functional study.
  Proteins, 37, 191-203.  
9914259 J.N.Jansonius (1998).
Structure, evolution and action of vitamin B6-dependent enzymes.
  Curr Opin Struct Biol, 8, 759-769.  
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 codes are shown on the right.