6NBL

Cytochrome P450cam-putidaredoxin complex bound to camphor and cyanide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Ligand and Redox Partner Binding Generates a New Conformational State in Cytochrome P450cam (CYP101A1).

Follmer, A.H.Tripathi, S.Poulos, T.L.

(2019) J. Am. Chem. Soc. 141: 2678-2683

  • DOI: 10.1021/jacs.8b13079

  • PubMed Abstract: 
  • It has become increasingly clear that cytochromes P450 can cycle back and forth between two extreme conformational states termed the closed and open states. In the well-studied cytochrome P450cam, the binding of its redox partner, putidaredoxin (Pdx) ...

    It has become increasingly clear that cytochromes P450 can cycle back and forth between two extreme conformational states termed the closed and open states. In the well-studied cytochrome P450cam, the binding of its redox partner, putidaredoxin (Pdx), shifts P450cam toward the open state. Shifting to the open state is thought to be important in the formation of a proton relay network essential for O-O bond cleavage and formation of the active Fe(IV)═O intermediate. Another important intermediate is the oxy-P450cam complex when bound to Pdx. Trapping this intermediate in crystallo is challenging owing to its instability, but the CN - complex is both stable and an excellent mimic of the O 2 complex. Here we present the P450cam-Pdx structure complexed with CN - . CN - results in large conformational changes including cis/trans isomerization of proline residues. Changes include large rearrangements of active-site residues and the formation of new active-site access channel that we have termed channel 2. The formation of channel 2 has also been observed in our previous molecular dynamics simulations wherein substrate binding to an allosteric site remote from the active site opens up channel 2. This new structure supports an extensive amount of previous work showing that distant regions of the structure are dynamically coupled and underscores the potentially important role that large conformational changes and dynamics play in P450 catalysis.


    Organizational Affiliation

    Department of Chemistry & Biochemistry , University of California , Santa Cruz , California 95064 , United States.,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, B
415Pseudomonas putidaMutation(s): 6 
Gene Names: camC (cyp101)
EC: 1.14.15.1
Find proteins for P00183 (Pseudomonas putida)
Go to UniProtKB:  P00183
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putidaredoxin
C, D
112Pseudomonas putidaMutation(s): 2 
Gene Names: camB
Find proteins for P00259 (Pseudomonas putida)
Go to UniProtKB:  P00259
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

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

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

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
C, D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
1N0
Query on 1N0

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Download CCD File 
C, D
1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione
bis(maleimido)hexane, bound form
C14 H20 N2 O4
PBFKSBAPGGMKKJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.360α = 90.00
b = 110.300β = 107.67
c = 88.620γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing

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 StatesGM057353

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release