5WK9

R186AP450cam with CN and camphor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.983 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Effect of Redox Partner Binding on Cytochrome P450 Conformational Dynamics.

Batabyal, D.Richards, L.S.Poulos, T.L.

(2017) J. Am. Chem. Soc. 139: 13193-13199

  • DOI: 10.1021/jacs.7b07656
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Previous crystal structures of cytochrome P450cam complexed with its redox partner, putidaredoxin (Pdx), shows that P450cam adopts the open conformation. It has been hypothesized that the Pdx-induced shift toward the open state frees the essential As ...

    Previous crystal structures of cytochrome P450cam complexed with its redox partner, putidaredoxin (Pdx), shows that P450cam adopts the open conformation. It has been hypothesized that the Pdx-induced shift toward the open state frees the essential Asp251 from salt bridges with Arg186 and Lys178 so that Asp251 can participate in a proton relay network required for O2 activation. This in part explains why P450cam has such a strict requirement for Pdx. One problem with this view is that looser substrate-protein interactions in the open state may not be compatible with the observed regio- and stereoselective hydroxylation. In the present study, molecular dynamics simulations show that Pdx binding favors a conformation that stabilizes the active site and decreases camphor mobility yet retains a partially open conformation compatible with the required proton relay network. The R186A mutant which frees Asp251 in the absence of Pdx retains good enzyme activity, and the crystal structure shows that product, 5-exo-hydroxycamphor, is bound. This indicates that rupture of the Asp251-Arg186 relaxes selectivity with respect to source of electrons and enables X-ray generated reducing equivalents to support substrate hydroxylation. These combined computational and experimental results are consistent with the proposed role of Pdx in assisting the release of Asp251 from ion pairs so that it can participate in proton-coupled electron transfer.


    Organizational Affiliation

    Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California , Irvine, California 92697-3900, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Camphor 5-monooxygenase
A
415Pseudomonas putidaMutation(s): 1 
Gene Names: camC (cyp101)
EC: 1.14.15.1
Find proteins for P00183 (Pseudomonas putida)
Go to UniProtKB:  P00183
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CYN
Query on CYN

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Download CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
CAM
Query on CAM

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Download CCD File 
A
CAMPHOR
C10 H16 O
DSSYKIVIOFKYAU-XCBNKYQSSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
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: 1.983 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.950α = 90.00
b = 58.860β = 104.99
c = 57.280γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
iMOSFLMdata reduction
PHENIXrefinement
pointlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM57353

Revision History 

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references