› 4y9d

X-ray diffraction
2.01Å resolution

Crystal structure of LigD in complex with NADH from Sphingobium sp. strain SYK-6

Released:
DOI: 10.2210/pdb4y9d/pdb
PDB entry 4y9d coloured by chain, front view.
PDB entry 4y9d coloured by chain, side view.
PDB entry 4y9d coloured by chain, top view.
Source organism: Sphingobium sp. SYK-6
Primary publication:
Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.
Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD
J Biol Chem 291 10228-38 (2016)
PMID: 26940872

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124249 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
C alpha-dehydrogenase Chain: A
Molecule details ›
Chain: A
Length: 305 amino acids
Theoretical weight: 32.38 KDa
Source organism: Sphingobium sp. SYK-6
Expression system: Escherichia coli
UniProt:
  • Canonical: G2IN91 (Residues: 1-305; Coverage: 100%)
Gene names: SLG_08640, ligD
Sequence domains: short chain dehydrogenase
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

1 bound ligand:
Ligand NAI 1 x NAI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P3121
Unit cell:
a: 61.762Å b: 61.762Å c: 134.713Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.215 0.211 0.248
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism.
Kamimura et al. (2017)
5 more

1 mention without citation

Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.
Pereira et al. (2016)