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X-ray diffraction
2.2Å resolution

CRYSTAL STRUCTURE OF P4 VARIANT OF BIPHENYL DIOXYGENASE FROM BURKHOLDERIA XENOVORANS LB400

Released:
DOI: 10.2210/pdb2xso/pdb
PDB entry 2xso coloured by chain, front view.
PDB entry 2xso coloured by chain, side view.
PDB entry 2xso coloured by chain, top view.
Source organism: Paraburkholderia xenovorans LB400
Primary publication:
Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution.
Kumar P, Mohammadi M, Viger JF, Barriault D, Gomez-Gil L, Eltis LD, Bolin JT, Sylvestre M
J Mol Biol 405 531-47 (2011)
PMID: 21073881

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, M, O, Q, S, U, W
Molecule details ›
Chains: A, C, E, G, I, K, M, O, Q, S, U, W
Length: 459 amino acids
Theoretical weight: 51.53 KDa
Source organism: Paraburkholderia xenovorans LB400
Expression system: Escherichia coli
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, N, P, R, T, V, X
Molecule details ›
Chains: B, D, F, H, J, L, N, P, R, T, V, X
Length: 188 amino acids
Theoretical weight: 22.11 KDa
Source organism: Paraburkholderia xenovorans LB400
Expression system: Escherichia coli
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

2 bound ligands:
Ligand FES 12 x FES
Ligand FE2 12 x FE2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P1
Unit cell:
a: 133.472Å b: 133.585Å c: 133.229Å
α: 102.51° β: 104.99° γ: 102.75°
R-values:
R R work R free
0.217 0.215 0.266
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Flavonoids biotransformation by bacterial non-heme dioxygenases, biphenyl and naphthalene dioxygenase.
Seo et al. (2011)
1 more

4 mentions without citation

Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution.
Kumar et al. (2011)
3 more