1BDB

CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE FROM PSEUDOMONAS SP. LB400


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 A resolution.

Hulsmeyer, M.Hecht, H.J.Niefind, K.Hofer, B.Eltis, L.D.Timmis, K.N.Schomburg, D.

(1998) Protein Sci. 7: 1286-1293

  • DOI: 10.1002/pro.5560070603

  • PubMed Abstract: 
  • cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+-enzyme complex was determined by molecular replacement and refined to an R-value of ...

    cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the aerobic biodegradation of polychlorinated biphenyls (PCBs). The crystal structure of the NAD+-enzyme complex was determined by molecular replacement and refined to an R-value of 17.9% at 2.0 A. As a member of the short-chain alcohol dehydrogenase/reductase (SDR) family, the overall protein fold and positioning of the catalytic triad in BphB are very similar to those observed in other SDR enzymes, although small differences occur in the cofactor binding site. Modeling studies indicate that the substrate is bound in a deep hydrophobic cleft close to the nicotinamide moiety of the NAD+ cofactor. These studies further suggest that Asn143 is a key determinant of substrate specificity. A two-step reaction mechanism is proposed for cis-dihydrodiol dehydrogenases.


    Related Citations: 
    • Genetic Analysis of a Pseudomonas Locus Encoding a Pathway for Biphenyl/Polychlorinated Biphenyl Degradation
      Hofer, B.,Eltis, L.D.,Dowling, D.N.,Timmis, K.N.
      (1993) Gene 130: 47


    Organizational Affiliation

    National Institute for Biotechnological Research (GBF), Department of Structure Research, Braunschweig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE
A
277Burkholderia xenovorans (strain LB400)Gene Names: bphB
EC: 1.3.1.56
Find proteins for P47227 (Burkholderia xenovorans (strain LB400))
Go to UniProtKB:  P47227
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.179 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.200α = 90.00
b = 79.200β = 90.00
c = 152.880γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance