4APY

Ethylene glycol-bound form of P450 CYP125A3 from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway.

Garcia-Fernandez, E.Frank, D.J.Galan, B.Kells, P.M.Podust, L.M.Garcia, J.L.Ortiz de Montellano, P.R.

(2013) Environ Microbiol 15: 2342

  • DOI: https://doi.org/10.1111/1462-2920.12108
  • Primary Citation of Related Structures:  
    2YOO, 3ZBY, 4APY

  • PubMed Abstract: 

    Degradation of the cholesterol side-chain in Mycobacterium tuberculosis is initiated by two cytochromes P450, CYP125A1 and CYP142A1, that sequentially oxidize C26 to the alcohol, aldehyde and acid metabolites. Here we report characterization of the homologous enzymes CYP125A3 and CYP142A2 from Mycobacterium smegmatis mc(2) 155. Heterologously expressed, purified CYP125A3 and CYP142A2 bound cholesterol, 4-cholesten-3-one, and antifungal azole drugs. CYP125A3 or CYP142A2 reconstituted with spinach ferredoxin and ferredoxin reductase efficiently hydroxylated 4-cholesten-3-one to the C-26 alcohol and subsequently to the acid. The X-ray structures of both substrate-free CYP125A3 and CYP142A2 and of cholest-4-en-3-one-bound CYP142A2 reveal significant differences in the substrate binding sites compared with the homologous M. tuberculosis proteins. Deletion only of cyp125A3 causes a reduction of both the alcohol and acid metabolites and a strong induction of cyp142 at the mRNA and protein levels, indicating that CYP142A2 serves as a functionally redundant back up enzyme for CYP125A3. In contrast to M. tuberculosis, the M. smegmatis Δcyp125Δcyp142 double mutant retains its ability to grow on cholesterol albeit with a diminished capacity, indicating an additional level of redundancy within its genome.


  • Organizational Affiliation

    Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P450 HEME-THIOLATE PROTEIN433Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1.14.15.29
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
E [auth A]
F [auth A]
G [auth A]
B [auth A],
C [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.188α = 90
b = 108.188β = 90
c = 120.234γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references
  • Version 1.2: 2013-08-14
    Changes: Database references
  • Version 1.3: 2018-02-07
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description