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PDBsum entry 1ars

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Transferase(aminotransferase) PDB id
1ars
Jmol
Contents
Protein chain
396 a.a. *
Ligands
PLP
Waters ×127
* Residue conservation analysis
PDB id:
1ars
Name: Transferase(aminotransferase)
Title: X-ray crystallographic study of pyridoxal 5'-phosphate-type aminotransferases from escherichia coli in open and closed
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)
Resolution:
1.80Å     R-factor:   0.213    
Authors: A.Okamoto,T.Higuchi,K.Hirotsu
Key ref: A.Okamoto et al. (1994). X-ray crystallographic study of pyridoxal 5'-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form. J Biochem, 116, 95. PubMed id: 7798192
Date:
02-Aug-93     Release date:   31-Aug-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 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
+ 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   2 terms 
  Biological process     biosynthetic process   4 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
J Biochem 116:95 (1994)
PubMed id: 7798192  
 
 
X-ray crystallographic study of pyridoxal 5'-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form.
A.Okamoto, T.Higuchi, K.Hirotsu, S.Kuramitsu, H.Kagamiyama.
 
  ABSTRACT  
 
We determined the three-dimensional structures of aspartate aminotransferase (AspAT) from Escherichia coli and its complex with inhibitor (2-methyl-L-aspartate) at 1.8A resolution. This enzyme reversibly catalyzes the transamination reaction and is a dimer of two identical subunits. Each subunit has 396 amino acid residues and one pyridoxal 5'-phosphate as a cofactor, and is divided into two domains, one large and the other small. Upon binding of the inhibitor, the small domain rotates by 5 degrees toward the large domain to close the active site. This domain movement is caused mainly by small but important main-chain conformational changes in the residues located over the domain interface of the small domain. In chicken mitochondrial AspAT, the domain movement was larger, with a rotational angle of 13 degrees. By comparison of these two structures, the difference in the rotational angles was found to be caused by the larger opening of the domain in the open form of chicken mitochondrial AspAT. Although the overall structures of these two enzymes were almost identical, the surface area of the domain interface in the E. coli enzyme was larger than that in mitochondrial AspAT, suggesting that the structure of the domain interface is responsible for the degree of movement of the small domain.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21332942 H.J.Wu, Y.Yang, S.Wang, J.Q.Qiao, Y.F.Xia, Y.Wang, W.D.Wang, S.F.Gao, J.Liu, P.Q.Xue, and X.W.Gao (2011).
Cloning, expression and characterization of a new aspartate aminotransferase from Bacillus subtilis B3.
  FEBS J, 278, 1345-1357.  
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
19640845 M.Goto, T.Yamauchi, N.Kamiya, I.Miyahara, T.Yoshimura, H.Mihara, T.Kurihara, K.Hirotsu, and N.Esaki (2009).
Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe.
  J Biol Chem, 284, 25944-25952.
PDB codes: 1wtc 2zr8
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.  
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
18366019 R.Z.Liao, W.J.Ding, J.G.Yu, W.H.Fang, and R.Z.Liu (2008).
Theoretical studies on pyridoxal 5'-phosphate-dependent transamination of alpha-amino acids.
  J Comput Chem, 29, 1919-1929.  
17683331 I.Matsui, and K.Harata (2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
  FEBS J, 274, 4012-4022.  
15889412 K.Hirotsu, M.Goto, A.Okamoto, and I.Miyahara (2005).
Dual substrate recognition of aminotransferases.
  Chem Rec, 5, 160-172.  
15189147 A.C.Eliot, and J.F.Kirsch (2004).
Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations.
  Annu Rev Biochem, 73, 383-415.  
  15803651 D.E.Ward, W.M.de Vos, and J.van der Oost (2002).
Molecular analysis of the role of two aromatic aminotransferases and a broad-specificity aspartate aminotransferase in the aromatic amino acid metabolism of Pyrococcus furiosus.
  Archaea, 1, 133-141.  
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.  
11248682 A.Matharu, H.Hayashi, H.Kagamiyama, B.Maras, and R.A.John (2001).
Contributions of the substrate-binding arginine residues to maleate-induced closure of the active site of Escherichia coli aspartate aminotransferase.
  Eur J Biochem, 268, 1640-1645.  
11933245 H.Kagamiyama, and H.Hayashi (2001).
Release of enzyme strain during catalysis reduces the activation energy barrier.
  Chem Rec, 1, 385-394.  
11148029 H.Mizuguchi, H.Hayashi, K.Okada, I.Miyahara, K.Hirotsu, and H.Kagamiyama (2001).
Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase.
  Biochemistry, 40, 353-360.
PDB codes: 1g4v 1g4x 1g7w 1g7x
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
11737206 R.Contestabile, A.Paiardini, S.Pascarella, M.L.di Salvo, S.D'Aguanno, and F.Bossa (2001).
l-Threonine aldolase, serine hydroxymethyltransferase and fungal alanine racemase. A subgroup of strictly related enzymes specialized for different functions.
  Eur J Biochem, 268, 6508-6525.  
10906409 F.S.Tahanejad, H.Naderi-Manesh, B.Habibinejad, and M.Mahmoudian (2000).
Homology-based molecular modelling of PLP-dependent histidine decarboxylase from Mmorganella morganii.
  Eur J Med Chem, 35, 567-576.  
10673430 G.Schneider, H.Käck, and Y.Lindqvist (2000).
The manifold of vitamin B6 dependent enzymes.
  Structure, 8, R1-R6.  
11112527 M.M.Islam, H.Hayashi, H.Mizuguchi, and H.Kagamiyama (2000).
The substrate activation process in the catalytic reaction of Escherichia coli aromatic amino acid aminotransferase.
  Biochemistry, 39, 15418-15428.  
10684605 T.Fujii, M.Maeda, H.Mihara, T.Kurihara, N.Esaki, and Y.Hata (2000).
Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase.
  Biochemistry, 39, 1263-1273.
PDB code: 1c0n
9930977 A.Okamoto, S.Ishii, K.Hirotsu, and H.Kagamiyama (1999).
The active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity.
  Biochemistry, 38, 1176-1184.
PDB codes: 2ay1 2ay2 2ay3 2ay4 2ay5 2ay6 2ay7 2ay8 2ay9
10387080 J.N.Scarsdale, G.Kazanina, S.Radaev, V.Schirch, and H.T.Wright (1999).
Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 A resolution: mechanistic implications.
  Biochemistry, 38, 8347-8358.
PDB code: 1cj0
10223296 K.A.Denessiouk, A.I.Denesyuk, J.V.Lehtonen, T.Korpela, and M.S.Johnson (1999).
Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes.
  Proteins, 35, 250-261.  
10029535 T.Nakai, K.Okada, S.Akutsu, I.Miyahara, S.Kawaguchi, R.Kato, S.Kuramitsu, and K.Hirotsu (1999).
Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate.
  Biochemistry, 38, 2413-2424.
PDB codes: 1bjw 1bkg
10417420 T.P.Ko, S.P.Wu, W.Z.Yang, H.Tsai, and H.S.Yuan (1999).
Crystallization and preliminary crystallographic analysis of the Escherichia coli tyrosine aminotransferase.
  Acta Crystallogr D Biol Crystallogr, 55, 1474-1477.
PDB code: 3tat
  10595543 W.Blankenfeldt, C.Nowicki, M.Montemartini-Kalisz, H.M.Kalisz, and H.J.Hecht (1999).
Crystal structure of Trypanosoma cruzi tyrosine aminotransferase: substrate specificity is influenced by cofactor binding mode.
  Protein Sci, 8, 2406-2417.
PDB code: 1bw0
  9655342 C.J.Jeffery, T.Barry, S.Doonan, G.A.Petsko, and D.Ringe (1998).
Crystal structure of Saccharomyces cerevisiae cytosolic aspartate aminotransferase.
  Protein Sci, 7, 1380-1387.
PDB code: 1yaa
9790670 H.Hayashi, H.Mizuguchi, and H.Kagamiyama (1998).
The imine-pyridine torsion of the pyridoxal 5'-phosphate Schiff base of aspartate aminotransferase lowers its pKa in the unliganded enzyme and is crucial for the successive increase in the pKa during catalysis.
  Biochemistry, 37, 15076-15085.  
9914259 J.N.Jansonius (1998).
Structure, evolution and action of vitamin B6-dependent enzymes.
  Curr Opin Struct Biol, 8, 759-769.  
  9761478 S.Pascarella, S.Angelaccio, R.Contestabile, S.Delle Fratte, M.Di Salvo, and F.Bossa (1998).
The structure of serine hydroxymethyltransferase as modeled by homology and validated by site-directed mutagenesis.
  Protein Sci, 7, 1976-1982.  
9576913 T.Yano, S.Oue, and H.Kagamiyama (1998).
Directed evolution of an aspartate aminotransferase with new substrate specificities.
  Proc Natl Acad Sci U S A, 95, 5511-5515.  
9012676 E.T.Mollova, D.E.Metzler, A.Kintanar, H.Kagamiyama, H.Hayashi, K.Hirotsu, and I.Miyahara (1997).
Use of 1H-15N heteronuclear multiple-quantum coherence NMR spectroscopy to study the active site of aspartate aminotransferase.
  Biochemistry, 36, 615-625.  
9354624 H.Hayashi, and H.Kagamiyama (1997).
Transient-state kinetics of the reaction of aspartate aminotransferase with aspartate at low pH reveals dual routes in the enzyme-substrate association process.
  Biochemistry, 36, 13558-13569.  
9365986 M.Petukhov, Y.Kil, S.Kuramitsu, and V.Lanzov (1997).
Insights into thermal resistance of proteins from the intrinsic stability of their alpha-helices.
  Proteins, 29, 309-320.  
8639626 H.Hayashi, K.Inoue, H.Mizuguchi, and H.Kagamiyama (1996).
Analysis of the substrate-recognition mode of aromatic amino acid aminotransferase by combined use of quasisubstrates and site-directed mutagenesis: systematic hydroxy-group addition/deletion studies to probe the enzyme-substrate interactions.
  Biochemistry, 35, 6754-6761.  
  8528072 J.J.Onuffer, B.T.Ton, I.Klement, and J.F.Kirsch (1995).
The use of natural and unnatural amino acid substrates to define the substrate specificity differences of Escherichia coli aspartate and tyrosine aminotransferases.
  Protein Sci, 4, 1743-1749.  
7556224 R.Graber, P.Kasper, V.N.Malashkevich, E.Sandmeier, P.Berger, H.Gehring, J.N.Jansonius, and P.Christen (1995).
Changing the reaction specificity of a pyridoxal-5'-phosphate-dependent enzyme.
  Eur J Biochem, 232, 686-690.
PDB codes: 1arg 1arh
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.