› 7ye3

X-ray diffraction
2.55Å resolution

Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with MES

Released:
DOI: 10.2210/pdb7ye3/pdb
PDB entry 7ye3 coloured by chain, front view.
PDB entry 7ye3 coloured by chain, side view.
PDB entry 7ye3 coloured by chain, top view.
Source organism: Lacticaseibacillus rhamnosus
Primary publication:
Crystal Structures of Lacticaseibacillus 4-Deoxy-L-threo-5-hexosulose-uronate Ketol-isomerase KduI in Complex with Substrate Analogs.
Iwase H, Yamamoto Y, Yamada A, Kawai K, Oiki S, Watanabe D, Mikami B, Takase R, Hashimoto W
J Appl Glycosci (1999) 70 99-107 (2023)
PMID: 38239764

Function and Biology Details

Reaction catalysed: 
5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-220388 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 289 amino acids
Theoretical weight: 33.33 KDa
Source organism: Lacticaseibacillus rhamnosus
Expression system: Escherichia coli
UniProt:
  • Canonical: C2JUP1 (Residues: 1-281; Coverage: 100%)
Gene names: HMPREF0539_0625, kduI
Sequence domains: KduI/IolB family

Ligands and Environments

2 bound ligands:
Ligand ZN 6 x ZN
Ligand MES 4 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: C2
Unit cell:
a: 93.035Å b: 189.102Å c: 114.852Å
α: 90° β: 107.12° γ: 90°
R-values:
R R work R free
0.196 0.193 0.256
Expression system: Escherichia coli

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