› 4z9y

X-ray diffraction
1.63Å resolution

Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Pectobacterium carotovorum

Released:
DOI: 10.2210/pdb4z9y/pdb
PDB entry 4z9y coloured by chain, front view.
PDB entry 4z9y coloured by chain, side view.
PDB entry 4z9y coloured by chain, top view.
Source organism: Pectobacterium carotovorum subsp. carotovorum
Primary publication:
Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity.
Takase R, Maruyama Y, Oiki S, Mikami B, Murata K, Hashimoto W
Proteins 84 934-47 (2016)
PMID: 27028675

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165397 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-deoxy-D-gluconate 3-dehydrogenase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 253 amino acids
Theoretical weight: 27.29 KDa
Source organism: Pectobacterium carotovorum subsp. carotovorum
Expression system: Escherichia coli BL21(DE3)
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

1 bound ligand:
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P21
Unit cell:
a: 68.728Å b: 72.655Å c: 99.048Å
α: 90° β: 90.81° γ: 90°
R-values:
R R work R free
0.173 0.172 0.199
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

4-Deoxy-l-erythro-5-hexoseulose Uronate (DEH) and DEH Reductase: Key Molecule and Enzyme for the Metabolism and Utilization of Alginate.
Kawai et al. (2022)
1 other article

1 mention without citation

Agarolytic Pathway in the Newly Isolated Aquimarina sp. Bacterial Strain ERC-38 and Characterization of a Putative β-agarase.
Kang et al. (2023)