PDBsum entry 1akc

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Transferase(aminotransferase) PDB id
Protein chain
401 a.a. *
Waters ×311
* Residue conservation analysis
PDB id:
Name: Transferase(aminotransferase)
Title: Structural basis for the catalytic activity of aspartate aminotransferase k258h lacking its pyridoxal-5'-phosphate- binding lysine residue
Structure: Aspartate aminotransferase. Chain: a. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: heart. Expressed in: unidentified. Expression_system_taxid: 32644
Biol. unit: Dimer (from PQS)
2.30Å     R-factor:   0.172    
Authors: V.N.Malashkevich,J.N.Jansonius
Key ref:
V.N.Malashkevich et al. (1995). Structural basis for the catalytic activity of aspartate aminotransferase K258H lacking the pyridoxal 5'-phosphate-binding lysine residue. Biochemistry, 34, 405-414. PubMed id: 7819232 DOI: 10.1021/bi00002a004
28-Feb-94     Release date:   31-Jul-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00508  (AATM_CHICK) -  Aspartate aminotransferase, mitochondrial
423 a.a.
401 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: 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 = PPE) matches with 57.00% similarity
   Enzyme class 2: E.C.  - Kynurenine--oxoglutarate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Reaction: L-kynurenine + 2-oxoglutarate = 4-(2-aminophenyl)-2,4-dioxobutanoate + L-glutamate
+ 2-oxoglutarate
= 4-(2-aminophenyl)-2,4-dioxobutanoate
+ L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   2 terms 
  Biological process     small molecule metabolic process   9 terms 
  Biochemical function     catalytic activity     8 terms  


DOI no: 10.1021/bi00002a004 Biochemistry 34:405-414 (1995)
PubMed id: 7819232  
Structural basis for the catalytic activity of aspartate aminotransferase K258H lacking the pyridoxal 5'-phosphate-binding lysine residue.
V.N.Malashkevich, J.Jäger, M.Ziak, U.Sauder, H.Gehring, P.Christen, J.N.Jansonius.
Chicken mitochondrial and Escherichia coli aspartate aminotransferases K258H, in which the active site lysine residue has been exchanged for a histidine residue, retain partial catalytic competence [Ziak et al. (1993) Eur. J. Biochem. 211, 475-484]. Mutant PLP and PMP holoenzymes and the complexes of the latter (E. coli enzyme) with sulfate and 2-oxoglutarate, as well as complexes of the mitochondrial apoenzyme with N-(5'-phosphopyridoxyl)-L-aspartate or N-(5'-phosphopyridoxyl)-L-glutamate, were crystallized and analyzed by means of X-ray crystallography in order to examine how the side chain of histidine 258 can substitute as a general acid/base catalyst of the aldimine-ketimine tautomerization in enzymic transamination. The structures have been solved and refined at resolutions between 2.1 and 2.8 A. Both the closed and the open conformations, identical to those of the wild-type enzyme, were observed, indicating that the mutant enzymes of both species exhibit the same conformational flexibility as the wild-type enzymes, although in AspAT K258H the equilibrium is somewhat shifted toward the open conformation. The replacement of the active site K258 by a histidine residue resulted only in local structural adaptations necessary to accommodate the imidazole ring. The catalytic competence of the mutant enzyme, which in the forward half-reaction is 0.1% of that of the wild-type enzyme, suggests that the imidazole group is involved in the aldimine-ketimine tautomerization. However, the imidazole ring of H258 is too far away from C alpha and C4' of the coenzyme-substrate adduct for direct proton transfer, suggesting that the 1,3-prototropic shift is mediated by a water molecule. Although there is enough space for a water molecule in this area, it has not been detected. Dynamic fluctuations of the protein matrix might transiently open a channel, giving a water molecule fleeting access to the active site.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18433062 C.J.Liao, K.H.Chin, C.H.Lin, P.S.Tsai, P.C.Lyu, C.C.Young, A.H.Wang, and S.H.Chou (2008).
Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus.
  Proteins, 73, 362-371.
PDB code: 2ze3
16790434 B.Golinelli-Pimpaneau, C.Lüthi, and P.Christen (2006).
Structural basis for D-amino acid transamination by the pyridoxal 5'-phosphate-dependent catalytic antibody 15A9.
  J Biol Chem, 281, 23969-23977.
PDB codes: 1wcb 2bmk
17137304 S.K.Hsu, H.H.Lo, C.H.Kao, D.S.Lee, and W.H.Hsu (2006).
Enantioselective synthesis of L-homophenylalanine by whole cells of recombinant Escherichia coli expressing L-aminoacylase and N-acylamino acid racemase genes from Deinococcus radiodurans BCRC12827.
  Biotechnol Prog, 22, 1578-1584.  
15801779 H.H.Lo, S.K.Hsu, W.D.Lin, N.L.Chan, and W.H.Hsu (2005).
Asymmetrical synthesis of L-homophenylalanine using engineered Escherichia coli aspartate aminotransferase.
  Biotechnol Prog, 21, 411-415.  
15210695 B.Cellini, M.Bertoldi, A.Paiardini, S.D'Aguanno, and C.B.Voltattorni (2004).
Site-directed mutagenesis provides insight into racemization and transamination of alanine catalyzed by Treponema denticola cystalysin.
  J Biol Chem, 279, 36898-36905.  
15226299 J.Singh, G.A.Khan, L.Kinarsky, H.Cheng, J.Wilken, K.H.Choi, E.Bedows, S.Sherman, and P.W.Cheng (2004).
Identification of disulfide bonds among the nine core 2 N-acetylglucosaminyltransferase-M cysteines conserved in the mucin beta6-N-acetylglucosaminyltransferase family.
  J Biol Chem, 279, 38969-38977.  
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.  
10545331 W.Grabarse, M.Vaupel, J.A.Vorholt, S.Shima, R.K.Thauer, A.Wittershagen, G.Bourenkov, H.D.Bartunik, and U.Ermler (1999).
The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri.
  Structure, 7, 1257-1268.
PDB code: 1qlm
9538014 D.Peisach, D.M.Chipman, P.W.Van Ophem, J.M.Manning, and D.Ringe (1998).
Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.
  Biochemistry, 37, 4958-4967.
PDB codes: 3daa 4daa
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.  
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