5WK9

R186AP450cam with CN and camphor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    5WK7, 5WK9

  • 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 Asp251 from salt bridges with Arg186 and Lys178 so that Asp251 can participate in a proton relay network required for O 2 activation ...

    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 O 2 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Camphor 5-monooxygenaseA415Pseudomonas putidaMutation(s): 1 
Gene Names: camCcyp101
EC: 1.14.15.1
UniProt
Find proteins for P00183 (Pseudomonas putida)
Explore P00183 
Go to UniProtKB:  P00183
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00183
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CAM
Query on CAM

Download Ideal Coordinates CCD File 
D [auth A]CAMPHOR
C10 H16 O
DSSYKIVIOFKYAU-XCBNKYQSSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CYN
Query on CYN

Download Ideal Coordinates CCD File 
C [auth A]CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CAM Binding MOAD:  5WK9 Kd: 3.22e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.95α = 90
b = 58.86β = 104.99
c = 57.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
pointlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM57353

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence