› 8gst

X-ray diffraction
1.71Å resolution

Crystal structure of L-2,4-diketo-3-deoxyrhamnonate hydrolase from Sphingomonas sp. (pyruvate bound-form)

Released:
DOI: 10.2210/pdb8gst/pdb
Model geometry
Fit model/data
PDB entry 8gst coloured by chain, front view.
PDB entry 8gst coloured by chain, side view.
PDB entry 8gst coloured by chain, top view.
Source organism: Sphingomonas sp. SKA58
Primary publication:
Crystal Structure of l-2,4-Diketo-3-deoxyrhamnonate Hydrolase Involved in the Nonphosphorylated l-Rhamnose Pathway from Bacteria.
Fukuhara S, Watanabe S, Watanabe Y, Nishiwaki H
Biochemistry 62 524-534 (2023)
PMID: 36563174

Function and Biology Details

Reaction catalysed: 
2,4-didehydro-3-deoxy-L-rhamnonate + H(2)O = pyruvate + (S)-lactate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-226953 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2,4-didehydro-3-deoxy-L-rhamnonate hydrolase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 296 amino acids
Theoretical weight: 32.34 KDa
Source organism: Sphingomonas sp. SKA58
Expression system: Escherichia coli DH5[alpha]
UniProt:
  • Canonical: Q1NEI7 (Residues: 2-285; Coverage: 100%)
Gene names: LRA6, SKA58_03585
Sequence domains: Fumarylacetoacetate (FAA) hydrolase family

Ligands and Environments

2 bound ligands:
Ligand MG 5 x MG
Ligand PYR 1 x PYR
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: P1
Unit cell:
a: 64.254Å b: 66.228Å c: 75.256Å
α: 90.27° β: 91.43° γ: 105.2°
R-values:
R R work R free
0.181 0.18 0.218
Expression system: Escherichia coli DH5[alpha]

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