2BMH

MODELING PROTEIN-SUBSTRATE INTERACTIONS IN THE HEME DOMAIN OF CYTOCHROME P450BM-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Modeling protein-substrate interactions in the heme domain of cytochrome P450(BM-3).

Li, H.Poulos, T.L.

(1995) Acta Crystallogr.,Sect.D 51: 21-32

  • DOI: 10.1107/S0907444994009194

  • PubMed Abstract: 
  • The crystal structure of heme domain of the fatty acid monooxygenase, cytochrome P450(BM-3), consisting of residues 1-455 has been independently solved to R = 0.18 at 2.0 A. The crystal form used, space group P2(1) with two molecules per asymmetric u ...

    The crystal structure of heme domain of the fatty acid monooxygenase, cytochrome P450(BM-3), consisting of residues 1-455 has been independently solved to R = 0.18 at 2.0 A. The crystal form used, space group P2(1) with two molecules per asymmetric unit, is isomorphous with that form with residues 1-471 first described by Boddupalli et al. [Boddupalli, Hasemann, Ravinchandran, Lu, Goldsmith, Deisenhofer & Peterson (1992). Proc. Natl Acad. Sci. USA, 89, 5567-5571] and used by Ravichandran, Boddupalli, Hasemann, Peterson & Deisenhofer [(1993). Science, 261, 731-736] to determine the crystal structure. The substrate-access channel consists of a large, hydrophobic cleft that appears to be the most likely route taken by fatty acid substrates. Attempts to soak crystals in mother liquor containing a variety of fatty acid substrates yielded featureless difference Fouriers even though fatty acid substrates are known to bind with dissociation constants in the micro M range. Modeling substrate-enzyme interactions reveals few contacts between the enzyme and substrate. More detailed modeling was carried out by subjecting both molecules in the asymmetric unit to extensive energy minimization. These studies reveal that the heme-domain active-site cleft can undergo a large conformational change that closes the access channel thereby providing enhanced protein-substrate interactions. These conformational changes are prevented from occurring by intermolecular contacts in the crystal lattice which lock the protein in the 'open' conformation.


    Related Citations: 
    • Structural Variation in Heme Enzymes: A Comparative Analysis of Peroxidase and P450 Crystal Structures
      Li, H.,Poulos, T.L.
      (1994) Structure 2: 461
    • Crystal Structure of Hemoprotein Domain of P450Bm-3, a Prototype for Microsomal P450S
      Ravichandran, K.G.,Boddupalli, S.S.,Hasemann, C.A.,Peterson, J.A.,Deisenhofer, J.
      (1993) Science 261: 731


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California at Irvine, 92717, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME P450 BM-3
A, B
455Bacillus 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: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.530α = 90.00
b = 154.030β = 94.97
c = 62.430γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1994-05-17 
  • Released Date: 1994-07-31 
  • Deposition Author(s): Li, H., Poulos, T.L.

Revision History 

  • Version 1.0: 1994-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance