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PDBsum entry 3daa

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protein ligands Protein-protein interface(s) links
Aminotransferase PDB id
3daa
Jmol
Contents
Protein chains
277 a.a. *
Ligands
PDD ×2
Waters ×253
* Residue conservation analysis
PDB id:
3daa
Name: Aminotransferase
Title: Crystallographic structure of d-amino acid aminotransferase inactivated by pyridoxyl-d-alanine
Structure: D-amino acid aminotransferase. Chain: a, b. Engineered: yes
Source: Bacillus sp.. Organism_taxid: 72579. Strain: ym-1. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.195     R-free:   0.245
Authors: D.Peisach,D.M.Chipman,D.Ringe
Key ref:
D.Peisach et al. (1998). Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase. Biochemistry, 37, 4958-4967. PubMed id: 9538014 DOI: 10.1021/bi972884d
Date:
20-Jan-98     Release date:   29-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19938  (DAAA_BACYM) -  D-alanine aminotransferase
Seq:
Struc:
283 a.a.
277 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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 = PDD) matches with 68.18% 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    
 
 
DOI no: 10.1021/bi972884d Biochemistry 37:4958-4967 (1998)
PubMed id: 9538014  
 
 
Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.
D.Peisach, D.M.Chipman, P.W.Van Ophem, J.M.Manning, D.Ringe.
 
  ABSTRACT  
 
The three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external aldimine, N-(5'-phosphopyridoxyl)-d-alanine (PPDA). Together with the previously reported pyridoxamine phosphate form of the enzyme [Sugio et al. (1995) Biochemistry 34, 9661], these structures allow us to describe the pathway of the enzymatic reaction in structural terms. A major determinant of the enzyme's stereospecificity for D-amino acids is a group of three residues (Tyr30, Arg98, and His100, with the latter two contributed by the neighboring subunit) forming four hydrogen bonds to the substrate alpha-carboxyl group. The replacement by hydrophobic groups of the homologous residues of the branched chain L-amino acid aminotransferase (which has a similar fold) could explain its opposite stereospecificity. As in L-aspartate aminotransferase (L-AspAT), the cofactor in D-aAT tilts (around its phosphate group and N1 as pivots) away from the catalytic lysine 145 and the protein face in the course of the reaction. Unlike L-AspAT, D-aAT shows no other significant conformational changes during the reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19923721 L.W.Tremblay, and J.S.Blanchard (2009).
The 1.9 A structure of the branched-chain amino-acid transaminase (IlvE) from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 1071-1077.
PDB code: 3ht5
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.  
18318836 M.Funakoshi, M.Sekine, M.Katane, T.Furuchi, M.Yohda, T.Yoshikawa, and H.Homma (2008).
Cloning and functional characterization of Arabidopsis thaliana D-amino acid aminotransferase--D-aspartate behavior during germination.
  FEBS J, 275, 1188-1200.  
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
16141215 M.Goto, I.Miyahara, K.Hirotsu, M.Conway, N.Yennawar, M.M.Islam, and S.M.Hutson (2005).
Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin.
  J Biol Chem, 280, 37246-37256.
PDB codes: 2a1h 2cog 2coi 2coj
15189147 A.C.Eliot, and J.F.Kirsch (2004).
Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations.
  Annu Rev Biochem, 73, 383-415.  
15302886 M.Noda, Y.Matoba, T.Kumagai, and M.Sugiyama (2004).
Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product.
  J Biol Chem, 279, 46153-46161.
PDB codes: 1vfh 1vfs 1vft
15128550 Y.Kawai, Y.Ishii, K.Arakawa, K.Uemura, B.Saitoh, J.Nishimura, H.Kitazawa, Y.Yamazaki, Y.Tateno, T.Itoh, and T.Saito (2004).
Structural and functional differences in two cyclic bacteriocins with the same sequences produced by lactobacilli.
  Appl Environ Microbiol, 70, 2906-2911.  
12777822 P.Kongsaeree, C.Samanchart, P.Laowanapiban, S.Wiyakrutta, and V.Meevootisom (2003).
Crystallization and preliminary X-ray crystallographic analysis of d-phenylglycine aminotransferase from Pseudomonas stutzeri ST201.
  Acta Crystallogr D Biol Crystallogr, 59, 953-954.  
11886871 A.Watanabe, T.Yoshimura, B.Mikami, H.Hayashi, H.Kagamiyama, and N.Esaki (2002).
Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine.
  J Biol Chem, 277, 19166-19172.
PDB codes: 1l6f 1l6g
12146963 O.Hur, D.Niks, P.Casino, and M.F.Dunn (2002).
Proton transfers in the beta-reaction catalyzed by tryptophan synthase.
  Biochemistry, 41, 9991.  
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
11933250 P.Christen, and P.K.Mehta (2001).
From cofactor to enzymes. The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes.
  Chem Rec, 1, 436-447.  
11106434 A.Gutierrez, T.Yoshimura, Y.Fuchikami, and N.Esaki (2000).
Modulation of activity and substrate specificity by modifying the backbone length of the distant interdomain loop of D-amino acid aminotransferase.
  Eur J Biochem, 267, 7218-7223.  
10630999 K.Kishimoto, C.Yasuda, and J.M.Manning (2000).
Reversible dissociation/association of D-amino acid transaminase subunits: properties of isolated active dimers and inactive monomers.
  Biochemistry, 39, 381-387.  
10079072 A.A.Morollo, G.A.Petsko, and D.Ringe (1999).
Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.
  Biochemistry, 38, 3293-3301.
PDB code: 2sfp
10508675 A.E.Todd, C.A.Orengo, and J.M.Thornton (1999).
Evolution of protein function, from a structural perspective.
  Curr Opin Chem Biol, 3, 548-556.  
10212188 G.A.Hunter, and G.C.Ferreira (1999).
Pre-steady-state reaction of 5-aminolevulinate synthase. Evidence for a rate-determining product release.
  J Biol Chem, 274, 12222-12228.  
9930994 P.W.van Ophem, D.Peisach, S.D.Erickson, K.Soda, D.Ringe, and J.M.Manning (1999).
Effects of the E177K mutation in D-amino acid transaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity.
  Biochemistry, 38, 1323-1331.
PDB code: 5daa
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 code is shown on the right.