1JPZ

Crystal structure of a complex of the heme domain of P450BM-3 with N-Palmitoylglycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pivotal role of water in the mechanism of P450BM-3.

Haines, D.C.Tomchick, D.R.Machius, M.Peterson, J.A.

(2001) Biochemistry 40: 13456-13465

  • Also Cited By: 3BEN

  • PubMed Abstract: 
  • Cytochrome P450s constitute a superfamily of enzymes that catalyze the oxidation of a vast number of structurally and chemically diverse hydrophobic substrates. Herein, we describe the crystal structure of a complex between the bacterial P450BM-3 and ...

    Cytochrome P450s constitute a superfamily of enzymes that catalyze the oxidation of a vast number of structurally and chemically diverse hydrophobic substrates. Herein, we describe the crystal structure of a complex between the bacterial P450BM-3 and the novel substrate N-palmitoylglycine at a resolution of 1.65 A, which reveals previously unrecognizable features of active site reorganization upon substrate binding. N-palmitoylglycine binds with higher affinity than any other known substrate and reacts with a higher turnover number than palmitic acid but with unaltered regiospecificity along the fatty acid moiety. Substrate binding induces conformational changes in distinct regions of the enzyme including part of the I-helix adjacent to the active site. These changes cause the displacement by about 1 A of the pivotal water molecule that ligands the heme iron, resulting in the low-spin to high-spin conversion of the iron. The water molecule is trapped close to the heme group, which allows it to partition between the iron and the new binding site. This partitioning explains the existence of a high-spin-low-spin equilibrium after substrate binding. The close proximity of the water molecule to the heme iron indicates that it may also participate in the proton-transfer cascade that leads to heterolytic bond scission of oxygen in P450BM-3.


    Related Citations: 
    • Structure of a cytochrome P450-redox partner electron-transfer complex
      Sevrioukova, I.F.,Li, H.,Zang, H.,Peterson, J.A.,Poulos, T.L.
      (1999) Proc.Natl.Acad.Sci.USA 96: 1863
    • The catalytic pathway of cytochrome p450cam at atomic resolution
      Schlichting, I.,Berendzen, J.,Chu, K.,Stock, A.M.,Maves, S.A.,Benson, D.E.,Sweet, R.M.,Ringe, D.,Petsko, G.A.,Sligar, S.G.
      (2000) Science 287: 1615
    • The structure of the cytochrome p450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid
      Li, H.,Poulos, T.L.
      (1997) Nat.Struct.Mol.Biol. 4: 140


    Organizational Affiliation

    Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9038, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIFUNCTIONAL P-450:NADPH-P450 REDUCTASE
A, B
473Bacillus 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
140
Query on 140

Download SDF File 
Download CCD File 
A, B
N-PALMITOYLGLYCINE
N-HEXADECANOYLGLYCINE
C18 H35 N O3
KVTFEOAKFFQCCX-UHFFFAOYSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
140Kd: 4 - 297 nM (99) BINDINGDB
140Kd: 262 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.190α = 90.00
b = 148.356β = 98.82
c = 64.134γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-09
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance