› 2yfl

X-ray diffraction
2.6Å resolution

Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran

Released:
DOI: 10.2210/pdb2yfl/pdb
PDB entry 2yfl coloured by chain, front view.
PDB entry 2yfl coloured by chain, side view.
PDB entry 2yfl coloured by chain, top view.
Source organism: Paraburkholderia xenovorans LB400
Primary publication:
Structural insights into the metabolism of 2-chlorodibenzofuran by an evolved biphenyl dioxygenase.
Kumar P, Mohammadi M, Dhindwal S, Pham TT, Bolin JT, Sylvestre M
Biochem Biophys Res Commun 421 757-62 (2012)
PMID: 22546558

Function and Biology Details

Reaction catalysed: 
Biphenyl + NADH + O(2) = (1S,2R)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD(+)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153396 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Biphenyl dioxygenase subunit alpha Chains: A, C, E, G, I, K
Molecule details ›
Chains: A, C, E, G, I, K
Length: 459 amino acids
Theoretical weight: 51.56 KDa
Source organism: Paraburkholderia xenovorans LB400
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P37333 (Residues: 1-459; Coverage: 100%)
Gene names: Bxe_C1197, Bxeno_C1131, bphA
Sequence domains:
Structure domains:
Biphenyl dioxygenase subunit beta Chains: B, D, F, H, J, L
Molecule details ›
Chains: B, D, F, H, J, L
Length: 188 amino acids
Theoretical weight: 22.11 KDa
Source organism: Paraburkholderia xenovorans LB400
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P37334 (Residues: 1-188; Coverage: 100%)
Gene names: Bxe_C1196, Bxeno_C1130, bphE
Sequence domains: Ring hydroxylating beta subunit
Structure domains: Nuclear Transport Factor 2; Chain: A,

Ligands and Environments

3 bound ligands:
Ligand FES 6 x FES
Ligand FE2 6 x FE2
Ligand DC4 2 x DC4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 86.556Å b: 275.982Å c: 92.057Å
α: 90° β: 117.46° γ: 90°
R-values:
R R work R free
0.218 0.215 0.28
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

Prospects for using combined engineered bacterial enzymes and plant systems to rhizoremediate polychlorinated biphenyls.
Sylvestre M. (2013)
6 other articles

1 mention without citation

Relationship between the binding free energy and PCBs' migration, persistence, toxicity and bioaccumulation using a combination of the molecular docking method and 3D-QSAR.
Zhao et al. (2018)