› 7c0e

X-ray diffraction
2.2Å resolution

Crystal structure of Azospirillum brasilense L-2-keto-3-deoxyarabonate dehydratase (2-oxobutyrate-bound form)

Released:
DOI: 10.2210/pdb7c0e/pdb
PDB entry 7c0e coloured by chain, front view.
PDB entry 7c0e coloured by chain, side view.
PDB entry 7c0e coloured by chain, top view.
Source organism: Azospirillum brasilense
Primary publication:
Biochemical and Structural Characterization of l-2-Keto-3-deoxyarabinonate Dehydratase: A Unique Catalytic Mechanism in the Class I Aldolase Protein Superfamily.
Watanabe S, Watanabe Y, Nobuchi R, Ono A
Biochemistry 59 2962-2973 (2020)
PMID: 32697085

Function and Biology Details

Reaction catalysed: 
2-dehydro-3-deoxy-L-arabinonate = 2,5-dioxopentanoate + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172909 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-2-keto-3-deoxyarabonate dehydratase Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 320 amino acids
Theoretical weight: 35.15 KDa
Source organism: Azospirillum brasilense
Expression system: Escherichia coli
UniProt:
  • Canonical: Q1JUQ0 (Residues: 2-309; Coverage: 100%)
Gene name: araD
Sequence domains: Dihydrodipicolinate synthetase family

Ligands and Environments

No bound ligands
1 modified residue:
Ligand FF9 12 x FF9

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: P1
Unit cell:
a: 74.524Å b: 81.198Å c: 142.835Å
α: 85.71° β: 88.43° γ: 75.39°
R-values:
R R work R free
0.224 0.221 0.269
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a α-furanosyl hemiketal of substrates.
Akagashi et al. (2024)

1 mention without citation

Structure and function of aldopentose catabolism enzymes involved in oxidative non-phosphorylative pathways.
Ren et al. (2022)