5DQN

Polyethylene 600-bound form of P450 CYP125A3 mutant from Myobacterium Smegmatis - W83Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Cytochrome P450 125A4, the Third Cholesterol C-26 Hydroxylase from Mycobacterium smegmatis.

Frank, D.J.Waddling, C.A.La, M.Ortiz de Montellano, P.R.

(2015) Biochemistry 54: 6909-6916

  • DOI: https://doi.org/10.1021/acs.biochem.5b01029
  • Primary Citation of Related Structures:  
    5DQN

  • PubMed Abstract: 

    Mycobacterium tuberculosis (Mtb) and Mycobacterium smegmatis (Msmeg) can grow on cholesterol as the sole carbon source. In Mtb the utilization of cholesterol can be initiated by CYP125A1 or CYP142A1 and in Msmeg by the orthologous CYP125A3 and CYP142A2. Double knockout of the two enzymes in Mtb prevents its growth on cholesterol, but the double knockout of Msmeg is still able to grow, albeit at a slower rate. We report here that Msmeg has a third enzyme, CYP125A4, that also oxidizes cholesterol, although it has a much higher activity for the oxidation of 7α-hydroxycholesterol. The ability of Msmeg CYP125A4 (and Mtb CYP125A1) to oxidize 7α-hydroxycholesterol is due, at least in part, to the presence of a smaller amino acid side chain facing C-7 of the sterol substrate than in CYP125A3. The ability to oxidize 7-substituted steroids broadens the range of sterol carbon sources for growth, but even more importantly in Mtb, additional biological effects are possible due to the potent immunomodulatory activity of 7α,26-dihydroxycholesterol.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158-2517, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 CYP125426Mycolicibacterium smegmatis MC2 155Mutation(s): 1 
Gene Names: cyp125MSMEI_5834
EC: 1.14.13.151
UniProt
Find proteins for A0R4Y3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R4Y3 
Go to UniProtKB:  A0R4Y3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R4Y3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.821α = 90
b = 108.821β = 90
c = 118.809γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

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 Allergy and Infectious Diseases (NIH/NIAID)United StatesAI074824

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description