spacer
spacer

PDBsum entry 1sff

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Transferase PDB id
1sff
Jmol
Contents
Protein chains
425 a.a. *
Ligands
SO4 ×11
EDO ×14
IK2 ×4
Waters ×1208
* Residue conservation analysis
PDB id:
1sff
Name: Transferase
Title: Structure of gamma-aminobutyrate aminotransferase complex with aminooxyacetate
Structure: 4-aminobutyrate aminotransferase. Chain: a, b, c, d. Synonym: gamma-amino-n-butyrate transaminase, gaba transaminase, glutamate:succinic semialdehyde transaminase, gaba aminotransferase, gaba-at. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: gabt, b2662. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.159     R-free:   0.186
Authors: W.Liu,P.E.Peterson,R.J.Carter,X.Zhou,J.A.Langston, A.J.Fisher,M.D.Toney
Key ref:
W.Liu et al. (2004). Crystal structures of unbound and aminooxyacetate-bound Escherichia coli gamma-aminobutyrate aminotransferase. Biochemistry, 43, 10896-10905. PubMed id: 15323550 DOI: 10.1021/bi049218e
Date:
19-Feb-04     Release date:   14-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P22256  (GABT_ECOLI) -  4-aminobutyrate aminotransferase GabT
Seq:
Struc:
426 a.a.
425 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.2.6.1.19  - 4-aminobutyrate--2-oxoglutarate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate
4-aminobutanoate
+
2-oxoglutarate
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
= succinate semialdehyde
+ L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
   Enzyme class 2: E.C.2.6.1.22  - (S)-3-amino-2-methylpropionate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: (S)-3-amino-2-methylpropanoate + 2-oxoglutarate = 2-methyl-3- oxopropanoate + L-glutamate
(S)-3-amino-2-methylpropanoate
+
2-oxoglutarate
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
= 2-methyl-3- oxopropanoate
+ L-glutamate
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!
  Biological process     gamma-aminobutyric acid metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi049218e Biochemistry 43:10896-10905 (2004)
PubMed id: 15323550  
 
 
Crystal structures of unbound and aminooxyacetate-bound Escherichia coli gamma-aminobutyrate aminotransferase.
W.Liu, P.E.Peterson, R.J.Carter, X.Zhou, J.A.Langston, A.J.Fisher, M.D.Toney.
 
  ABSTRACT  
 
The X-ray crystal structures of Escherichia coli gamma-aminobutyrate aminotransferase unbound and bound to the inhibitor aminooxyacetate are reported. The enzyme crystallizes from ammonium sulfate solutions in the P3(2)21 space group with a tetramer in the asymmetric unit. Diffraction data were collected to 2.4 A resolution for the unliganded enzyme and 1.9 A resolution for the aminooxyacetate complex. The overall structure of the enzyme is similar to those of other aminotransferase subgroup II enzymes. The ability of gamma-aminobutyrate aminotransferase to act on primary amine substrates (gamma-aminobutyrate) in the first half-reaction and alpha-amino acids in the second is proposed to be enabled by the presence of Glu211, whose side chain carboxylate alternates between interactions with Arg398 in the primary amine half-reaction and an alternative binding site in the alpha-amino acid half-reaction, in which Arg398 binds the substrate alpha-carboxylate. The specificity for a carboxylate group on the substrate side chain is due primarily to the presence of Arg141, but also requires substantial local main chain rearrangements relative to the structurally homologous enzyme dialkylglycine decarboxylase, which is specific for small alkyl side chains. No iron-sulfur cluster is found in the bacterial enzyme as was found in the pig enzyme [Storici, P., De Biase, D., Bossa, F., Bruno, S., Mozzarelli, A., Peneff, C., Silverman, R. B., and Schirmer, T. (2004) J. Biol. Chem. 279, 363-73.]. The binding of aminooxyacetate causes remarkably small changes in the active site structure, and no large domain movements are observed. Active site structure comparisons with pig gamma-aminobutyrate aminotransferase and dialkylglycine decarboxylase are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19997759 M.A.Khomutov, S.Mandal, J.Weisell, N.Saxena, A.R.Simonian, J.Vepsalainen, R.Madhubala, and S.N.Kochetkov (2010).
Novel convenient synthesis of biologically active esters of hydroxylamine.
  Amino Acids, 38, 509-517.  
19648235 J.Mayer, and A.M.Cook (2009).
Homotaurine metabolized to 3-sulfopropanoate in Cupriavidus necator H16: enzymes and genes in a patchwork pathway.
  J Bacteriol, 191, 6052-6058.  
19264755 S.M.Clark, R.Di Leo, P.K.Dhanoa, O.R.Van Cauwenberghe, R.T.Mullen, and B.J.Shelp (2009).
Biochemical characterization, mitochondrial localization, expression, and potential functions for an Arabidopsis gamma-aminobutyrate transaminase that utilizes both pyruvate and glyoxylate.
  J Exp Bot, 60, 1743-1757.  
17680656 B.K.Cho, H.Y.Park, J.H.Seo, J.Kim, T.J.Kang, B.S.Lee, and B.G.Kim (2008).
Redesigning the substrate specificity of omega-aminotransferase for the kinetic resolution of aliphatic chiral amines.
  Biotechnol Bioeng, 99, 275-284.  
18782763 E.D.Hopper, A.M.Pittman, M.C.Fitzgerald, and C.L.Tucker (2008).
In Vivo and in Vitro Examination of Stability of Primary Hyperoxaluria-associated Human Alanine:Glyoxylate Aminotransferase.
  J Biol Chem, 283, 30493-30502.  
17355287 G.Andersen, B.Andersen, D.Dobritzsch, K.D.Schnackerz, and J.Piskur (2007).
A gene duplication led to specialized gamma-aminobutyrate and beta-alanine aminotransferase in yeast.
  FEBS J, 274, 1804-1817.  
17259358 J.Kim, D.Kyung, H.Yun, B.K.Cho, J.H.Seo, M.Cha, and B.G.Kim (2007).
Cloning and characterization of a novel beta-transaminase from Mesorhizobium sp. strain LUK: a new biocatalyst for the synthesis of enantiomerically pure beta-amino acids.
  Appl Environ Microbiol, 73, 1772-1782.  
  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.  
15703173 A.Tocilj, J.D.Schrag, Y.Li, B.L.Schneider, L.Reitzer, A.Matte, and M.Cygler (2005).
Crystal structure of N-succinylarginine dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia coli.
  J Biol Chem, 280, 15800-15808.
PDB codes: 1ynf 1ynh 1yni
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.