› 6vvh

X-ray diffraction
1.79Å resolution

Arabidopsis thaliana dihydrodipicolinate synthase isoform 1 (DHDPS1) in complex with lysine

Released:
DOI: 10.2210/pdb6vvh/pdb
PDB entry 6vvh coloured by chain, front view.
PDB entry 6vvh coloured by chain, side view.
PDB entry 6vvh coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms.
Hall CJ, Lee M, Boarder MP, Mangion AM, Gendall AR, Panjikar S, Perugini MA, Soares da Costa TP
FEBS J 288 4973-4986 (2021)
PMID: 33586321

Function and Biology Details

Reaction catalysed: 
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192353 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic Chains: AAA, BBB, CCC, DDD
Molecule details ›
Chains: AAA, BBB, CCC, DDD
Length: 321 amino acids
Theoretical weight: 35.54 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9LZX6 (Residues: 49-365; Coverage: 87%)
Gene names: At3g60880, DHDPS, DHDPS1, DHPS1, T4C21_290
Sequence domains: Dihydrodipicolinate synthetase family

Ligands and Environments

4 bound ligands:
Ligand LYS 4 x LYS
Ligand NA 4 x NA
Ligand GOL 3 x GOL
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P212121
Unit cell:
a: 95.044Å b: 97.626Å c: 176.543Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.167 0.166 0.196
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 citation in other articles

A dual-target herbicidal inhibitor of lysine biosynthesis.
Mackie et al. (2022)
2 more

2 mentions without citation

Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants.
Soares da Costa et al. (2021)
1 more

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