3BEN

Structure of N-(12-imidazolyl-dodecanoyl)-L-leucine inhibitor bound to the heme domain of Cytochrome P450-BM3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of inhibitor-bound P450BM-3 reveals open conformation of substrate access channel.

Haines, D.C.Chen, B.Tomchick, D.R.Bondlela, M.Hegde, A.Machius, M.Peterson, J.A.

(2008) Biochemistry 47: 3662-3670

  • DOI: 10.1021/bi7023964

  • PubMed Abstract: 
  • P450BM-3 is an extensively studied P450 cytochrome that is naturally fused to a cytochrome P450 reductase domain. Crystal structures of the heme domain of this enzyme have previously generated many insights into features of P450 structure, substrate ...

    P450BM-3 is an extensively studied P450 cytochrome that is naturally fused to a cytochrome P450 reductase domain. Crystal structures of the heme domain of this enzyme have previously generated many insights into features of P450 structure, substrate binding specificity, and conformational changes that occur on substrate binding. Although many P450s are inhibited by imidazole, this compound does not effectively inhibit P450BM-3. Omega-imidazolyl fatty acids have previously been found to be weak inhibitors of the enzyme and show some unusual cooperativity with the substrate lauric acid. We set out to improve the properties of these inhibitors by attaching the omega-imidazolyl fatty acid to the nitrogen of an amino acid group, a tactic that we used previously to increase the potency of substrates. The resulting inhibitors were significantly more potent than their parent compounds lacking the amino acid group. A crystal structure of one of the new inhibitors bound to the heme domain of P450BM-3 reveals that the mode of interaction of the amino acid group with the enzyme is different from that previously observed for acyl amino acid substrates. Further, required movements of residues in the active site to accommodate the imidazole group provide an explanation for the low affinity of imidazole itself. Finally, the previously observed cooperativity with lauric acid is explained by a surprisingly open substrate-access channel lined with hydrophobic residues that could potentially accommodate lauric acid in addition to the inhibitor itself.


    Related Citations: 
    • 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
    • Interactions of Substrates at the Surface of P450s Can Greatly Enhance Substrate Potency
      Hegde, A.,Haines, D.C.,Bondlela, M.,Chen, B.,Schaffer, N.,Tomchick, D.R.,Machius, M.,Nguyen, H.,Chowdhary, P.K.,Peterson, J.A.
      () TO BE PUBLISHED --: --
    • Imidazolyl carboxylic acids as mechanistic probes of flavocytochrome P-450 BM3.
      Noble, M.A.,Quaroni, L.,Chumanov, G.D.,Turner, K.L.,Chapman, S.K.,Hanzlik, R.P.,Munro, A.W.
      (1998) Biochemistry 37: 15799


    Organizational Affiliation

    Department of Chemistry, The University of Texas at Dallas, Dallas, Texas 75083-0688, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 102
A, B
470Bacillus 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LEH
Query on LEH

Download SDF File 
Download CCD File 
A, B
N-[12-(1H-imidazol-1-yl)dodecanoyl]-L-leucine
C21 H37 N3 O3
PSJOKLGFODYIHJ-IBGZPJMESA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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
MES
Query on MES

Download SDF File 
Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LEHKd: 320 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.820α = 90.00
b = 148.209β = 98.32
c = 63.792γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-11-19 
  • Released Date: 2008-09-30 
  • Deposition Author(s): Tomchick, D.R.

Revision History 

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance