6WPL

Structure of Cytochrome P450tcu


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Unexpected Differences between Two Closely Related Bacterial P450 Camphor Monooxygenases.

Murarka, V.C.Batabyal, D.Amaya, J.A.Sevrioukova, I.F.Poulos, T.L.

(2020) Biochemistry 59: 2743-2750

  • DOI: 10.1021/acs.biochem.0c00366
  • Primary Citation of Related Structures:  
    6WPL

  • PubMed Abstract: 
  • The bacterial cytochrome P450cam catalyzes the oxidation of camphor to 5- exo -hydroxycamphor as the first step in the oxidative assimilation of camphor as a carbon/energy source. CYP101D1 is another bacterial P450 that catalyzes the same reaction ...

    The bacterial cytochrome P450cam catalyzes the oxidation of camphor to 5- exo -hydroxycamphor as the first step in the oxidative assimilation of camphor as a carbon/energy source. CYP101D1 is another bacterial P450 that catalyzes the same reaction. A third P450 (P450tcu) has recently been discovered that has ≈86% sequence identity to P450cam as well as very similar enzymatic properties. P450tcu, however, exhibits three unusual features not found in P450cam. First, we observe product in at least two orientations in the X-ray structure that indicates that, unlike the case for P450cam, X-ray-generated reducing equivalents can drive substrate hydroxylation in crystallo . We postulate, on the basis of molecular dynamics simulations, that greater flexibility in P450tcu enables easier access of protons to the active site and, together with X-ray driven reduction, results in O 2 activation and substrate hydroxylation. Second, the characteristic low-spin to high-spin transition when camphor binds occurs immediately with P450cam but is very slow in P450tcu. Third, isothermal titration calorimetry shows that in P450cam substrate binding is entropically driven with a Δ H of >0 while in P450tcu with a Δ H of <0 with a more modest change in - T Δ S . These results indicate that despite nearly identical structures and enzymatic properties, these two P450s exhibit quite different properties most likely related to differences in conformational dynamics.


    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P-450cam, subunit of camphor 5-monooxygenase systemA415Pseudomonas sp. TCU-HL1Mutation(s): 0 
Gene Names: THL1_4171
Find proteins for A0A1B3EAY9 (Pseudomonas sp. TCU-HL1)
Explore A0A1B3EAY9 
Go to UniProtKB:  A0A1B3EAY9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 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
CAH
Query on CAH

Download Ideal Coordinates CCD File 
C [auth A]5-EXO-HYDROXYCAMPHOR
C10 H16 O2
DJQYBVLXBVJHMU-PJKMHFRUSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.42α = 90
b = 56.993β = 90
c = 189.373γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesGM131920
National Institutes of Health/Office of the DirectorUnited StatesES025767

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references, Derived calculations