PDBsum entry 1amq

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Transferase(aminotransferase) PDB id
Protein chain
396 a.a. *
Waters ×258
* Residue conservation analysis
PDB id:
Name: Transferase(aminotransferase)
Title: X-ray crystallographic study of pyridoxamine 5'-phosphate-ty aspartate aminotransferases from escherichia coli in three
Structure: Aspartate aminotransferase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
2.20Å     R-factor:   0.192    
Authors: I.Miyahara,K.Hirotsu,H.Hayashi,H.Kagamiyama
Key ref: I.Miyahara et al. (1994). X-ray crystallographic study of pyridoxamine 5'-phosphate-type aspartate aminotransferases from Escherichia coli in three forms. J Biochem, 116, 1001-1012. PubMed id: 7896726
01-Jul-94     Release date:   30-Sep-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00509  (AAT_ECOLI) -  Aspartate aminotransferase
396 a.a.
396 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Aspartate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
+ 2-oxoglutarate
= oxaloacetate
+ L-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!
  Cellular component     cytoplasm   2 terms 
  Biological process     biosynthetic process   4 terms 
  Biochemical function     catalytic activity     8 terms  


J Biochem 116:1001-1012 (1994)
PubMed id: 7896726  
X-ray crystallographic study of pyridoxamine 5'-phosphate-type aspartate aminotransferases from Escherichia coli in three forms.
I.Miyahara, K.Hirotsu, H.Hayashi, H.Kagamiyama.
The three-dimensional structures of pyridoxamine 5'-phosphate-type aspartate aminotransferase from Escherichia coli and its complexes with maleate and glutarate have been determined by X-ray crystallography at 2.2, 2.1, and 2.7 A resolution, respectively. The enzyme is a dimeric form comprising two identical subunits, each of which is divided into one large and one small domain. The complex with maleate showed that substrate (or inhibitor) binding induced a large conformational change from the "open" to the "closed" form, resulting in closure of the active site by the small domain movement, as was observed in the pyridoxal 5'-phosphate-type enzyme. In the open form, three hydrophobic residues (hydrophobic plug) at the entrance of the active site are exposed to solvent. Maleate binding make the active site more hydrophobic by charge compensation and release of water molecules, facilitating the movement of the hydrophobic plug into the active site pocket to induce a large conformational change in the enzyme. Maleate is fixed rigidly in the active site pocket by extensive salt bridges and a hydrogen bonding network, guaranteeing the stereo-specificity of the catalysis and giving a Michaelis complex model. Contrary to our expectation, the glutarate complex was in the open form, suggesting that the equilibrium between the open and closed forms lies far toward the open form in solution. The water molecules located in the active site pocket were almost completely conserved between Escherichia coli and chicken mitochondrial aspartate aminotransferase with the same type of cofactor and the same conformation.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19826765 Q.Han, T.Cai, D.A.Tagle, and J.Li (2010).
Structure, expression, and function of kynurenine aminotransferases in human and rodent brains.
  Cell Mol Life Sci, 67, 353-368.
PDB code: 3hlm
18620547 Q.Han, T.Cai, D.A.Tagle, H.Robinson, and J.Li (2008).
Substrate specificity and structure of human aminoadipate aminotransferase/kynurenine aminotransferase II.
  Biosci Rep, 28, 205-215.
PDB code: 3dc1
18186649 Q.Han, Y.G.Gao, H.Robinson, and J.Li (2008).
Structural insight into the mechanism of substrate specificity of aedes kynurenine aminotransferase.
  Biochemistry, 47, 1622-1630.
PDB codes: 2r5c 2r5e
  16754985 S.M.Tripathi, and R.Ramachandran (2006).
Overexpression, purification and crystallization of lysine epsilon-aminotransferase (Rv3290c) from Mycobacterium tuberculosis H37Rv.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 572-575.  
15889412 K.Hirotsu, M.Goto, A.Okamoto, and I.Miyahara (2005).
Dual substrate recognition of aminotransferases.
  Chem Rec, 5, 160-172.  
12723595 H.Kim, K.Ikegami, M.Nakaoka, M.Yagi, H.Shibata, and Y.Sawa (2003).
Characterization of aspartate aminotransferase from the cyanobacterium Phormidium lapideum.
  Biosci Biotechnol Biochem, 67, 490-498.  
11752307 Y.Wang, J.B.Anderson, J.Chen, L.Y.Geer, S.He, D.I.Hurwitz, C.A.Liebert, T.Madej, G.H.Marchler, A.Marchler-Bauer, A.R.Panchenko, B.A.Shoemaker, J.S.Song, P.A.Thiessen, R.A.Yamashita, and S.H.Bryant (2002).
MMDB: Entrez's 3D-structure database.
  Nucleic Acids Res, 30, 249-252.  
11294630 K.Haruyama, T.Nakai, I.Miyahara, K.Hirotsu, H.Mizuguchi, H.Hayashi, and H.Kagamiyama (2001).
Structures of Escherichia coli histidinol-phosphate aminotransferase and its complexes with histidinol-phosphate and N-(5'-phosphopyridoxyl)-L-glutamate: double substrate recognition of the enzyme.
  Biochemistry, 40, 4633-4644.
PDB codes: 1gew 1gex 1gey
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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