› 3tmq

X-ray diffraction
2.1Å resolution

Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei in complex with D-arabinose-5-phosphate

Released:
DOI: 10.2210/pdb3tmq/pdb
PDB entry 3tmq coloured by chain, front view.
PDB entry 3tmq coloured by chain, side view.
PDB entry 3tmq coloured by chain, top view.
Source organism: Burkholderia pseudomallei 1710b
Primary publication:
Combining functional and structural genomics to sample the essential Burkholderia structome.
Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC
OpenAccess logo PLoS One 8 e53851 (2013)
PMID: 23382856

Function and Biology Details

Reaction catalysed: 
Phosphoenolpyruvate + D-arabinose 5-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174652 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-dehydro-3-deoxyphosphooctonate aldolase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 285 amino acids
Theoretical weight: 30.49 KDa
Source organism: Burkholderia pseudomallei 1710b
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q3JP68 (Residues: 1-281; Coverage: 100%)
Gene names: BURPS1710b_3264, kdsA
Sequence domains: DAHP synthetase I family
Structure domains: Aldolase class I

Ligands and Environments

3 bound ligands:
Ligand A5P 2 x A5P
Ligand NO3 10 x NO3
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P212121
Unit cell:
a: 89.72Å b: 92.08Å c: 152.98Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.179 0.217
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 review citations

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product.
Dailey et al. (2017)
10 more

1 mention without citation

Combining functional and structural genomics to sample the essential Burkholderia structome.
Baugh et al. (2013)