› 2z20

X-ray diffraction
1.95Å resolution

Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana

Released:
DOI: 10.2210/pdb2z20/pdb
PDB entry 2z20 coloured by chain, front view.
PDB entry 2z20 coloured by chain, side view.
PDB entry 2z20 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia.
Watanabe N, Cherney MM, van Belkum MJ, Marcus SL, Flegel MD, Clay MD, Deyholos MK, Vederas JC, James MN
J Mol Biol 371 685-702 (2007)
PMID: 17583737

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: 47.94 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


Cofactor: Ligand PLP 2 x PLP
2 bound ligands:
Ligand SO4 2 x SO4
Ligand GOL 4 x GOL
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P3221
Unit cell:
a: 102.909Å b: 102.909Å c: 171.452Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.184 0.182 0.227
Expression system: Escherichia coli

Quick links

Citations

24 citation in other articles

SubMAP: aligning metabolic pathways with subnetwork mappings.
Ay et al. (2011)
23 more

2 mentions without citation

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