2HPD

CRYSTAL STRUCTURE OF HEMOPROTEIN DOMAIN OF P450BM-3, A PROTOTYPE FOR MICROSOMAL P450'S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's.

Ravichandran, K.G.Boddupalli, S.S.Hasermann, C.A.Peterson, J.A.Deisenhofer, J.

(1993) Science 261: 731-736


  • PubMed Abstract: 
  • Cytochrome P450BM-3, a bacterial fatty acid monoxygenase, resembles the eukaryotic microsomal P450's and their flavoprotein reductase in primary structure and function. The three-dimensional structure of the hemoprotein domain of P450BM-3 was determi ...

    Cytochrome P450BM-3, a bacterial fatty acid monoxygenase, resembles the eukaryotic microsomal P450's and their flavoprotein reductase in primary structure and function. The three-dimensional structure of the hemoprotein domain of P450BM-3 was determined by x-ray diffraction and refined to an R factor of 16.9 percent at 2.0 angstrom resolution. The structure consists of an alph and a beta domain. The active site heme is accessible through a long hydrophobic channel formed primarily by the beta domain and the B' and F helices of the alpha domain. The two molecules in the asymmetric unit differ in conformation around the substrate binding pocket. Substantial differences between P450BM-3 and P450cam, the only other P450 structure available, are observed around the substrate binding pocket and the regions important for redox partner binding. A general mechanism for proton transfer in P450's is also proposed.


    Related Citations: 
    • P450Bm-3 and Other Inducible Bacterial P450 Cytochromes: Biochemistry and Regulation
      Fulco, A.J.
      (1991) Annu.Rev.Pharmacol.Toxicol. 31: 177
    • Crystallization and Preliminary X-Ray Diffraction Analysis of P450Terp and the Hemoprotein Domain of P450Bm-3, Enzymes Belonging to Two Distinct Classes of the Cytochrome P450 Superfamily
      Boddupalli, S.S.,Hasemann, C.A.,Ravichandran, K.G.,Lu, J.-Y.,Goldsmith, E.J.,Deisenhofer, J.,Peterson, J.A.
      (1992) Proc.Natl.Acad.Sci.USA 89: 5567


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75235-9050.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME P450 BM-3
A, B
471Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512)Mutation(s): 0 
Gene Names: cyp102A1 (cyp102)
Find proteins for P14779 (Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512))
Go to UniProtKB:  P14779
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.400α = 90.00
b = 154.000β = 94.70
c = 62.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance