› 3ei5

X-ray diffraction
2.05Å resolution

Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with PLP-Glu: an external aldimine mimic

Released:
DOI: 10.2210/pdb3ei5/pdb
PDB entry 3ei5 coloured by chain, front view.
PDB entry 3ei5 coloured by chain, side view.
PDB entry 3ei5 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana.
Watanabe N, Clay MD, van Belkum MJ, Cherney MM, Vederas JC, James MN
J Mol Biol 384 1314-29 (2008)
PMID: 18952095

Function and Biology Details

Reaction catalysed: 
LL-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + L-glutamate + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188172 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
LL-diaminopimelate aminotransferase, chloroplastic Chains: A, B
Molecule details ›
Chains: A, B
Length: 432 amino acids
Theoretical weight: 47.52 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93ZN9 (Residues: 36-461; Coverage: 92%)
Gene names: AGD2, At4g33680, DAP, T16L1.170
Sequence domains: Aminotransferase class I and II
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand PGU 2 x PGU
Ligand GOL 4 x GOL
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P3221
Unit cell:
a: 102.556Å b: 102.556Å c: 171.953Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.173 0.17 0.221
Expression system: Escherichia coli

Quick links

Citations

10 citation in other articles

L,L-diaminopimelate aminotransferase from Chlamydomonas reinhardtii: a target for algaecide development.
Dobson et al. (2011)
9 more

1 mention without citation

Structural analysis and mutant growth properties reveal distinctive enzymatic and cellular roles for the three major L-alanine transaminases of Escherichia coli.
Peña-Soler et al. (2014)