› 5k1k

X-ray diffraction
1.3Å resolution

Crystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) in complex with p-hydroxybenzaldehyde

Released:
DOI: 10.2210/pdb5k1k/pdb
PDB entry 5k1k coloured by chain, front view.
PDB entry 5k1k coloured by chain, side view.
PDB entry 5k1k coloured by chain, top view.
Source organism: Shewanella oneidensis MR-1
Primary publication:
Structural dissection of Shewanella oneidensis old yellow enzyme 4 bound to a Meisenheimer complex and (nitro)phenolic ligands.
Elegheert J, Brigé A, Van Beeumen J, Savvides SN
FEBS Lett 591 3391-3401 (2017)
PMID: 28869767

Function and Biology Details

Reaction catalysed: 
Reduced riboflavin + NADP(+) = riboflavin + NADPH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184340 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 355 amino acids
Theoretical weight: 39.13 KDa
Source organism: Shewanella oneidensis MR-1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8EBV3 (Residues: 1-355; Coverage: 100%)
Gene names: SO_3392, sye4
Sequence domains: NADH:flavin oxidoreductase / NADH oxidase family
Structure domains: Aldolase class I

Ligands and Environments


Cofactor: Ligand FMN 1 x FMN
2 bound ligands:
Ligand HBA 5 x HBA
Ligand 8K6 1 x 8K6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P212121
Unit cell:
a: 52.09Å b: 54.66Å c: 103.75Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.122 0.122 0.148
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

The Isoenzymic Diketocamphane Monooxygenases of Pseudomonas putida ATCC 17453-An Episodic History and Still Mysterious after 60 Years.
Willetts A. (2021)
1 other article

1 mention without citation

Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase η.
Patra et al. (2016)