2WM4

X-ray structure of Mycobacterium tuberculosis cytochrome P450 CYP124 in complex with phytanic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

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This is version 1.3 of the entry. See complete history


Literature

Biochemical and structural characterization of CYP124: a methyl-branched lipid omega-hydroxylase from Mycobacterium tuberculosis.

Johnston, J.B.Kells, P.M.Podust, L.M.Ortiz de Montellano, P.R.

(2009) Proc Natl Acad Sci U S A 106: 20687-20692

  • DOI: https://doi.org/10.1073/pnas.0907398106
  • Primary Citation of Related Structures:  
    2WM4, 2WM5

  • PubMed Abstract: 

    Mycobacterium tuberculosis (Mtb) produces a variety of methyl-branched lipids that serve important functions, including modulating the immune response during pathogenesis and contributing to a robust cell wall that is impermeable to many chemical agents. Here, we report characterization of Mtb CYP124 (Rv2266) that includes demonstration of preferential oxidation of methyl-branched lipids. Spectrophotometric titrations and analysis of reaction products indicate that CYP124 tightly binds and hydroxylates these substrates at the chemically disfavored omega-position. We also report X-ray crystal structures of the ligand-free and phytanic acid-bound protein at a resolution of 1.5 A and 2.1 A, respectively, which provide structural insights into a cytochrome P450 with predominant omega-hydroxylase activity. The structures of ligand-free and substrate-bound CYP124 reveal several differences induced by substrate binding, including reorganization of the I helix and closure of the active site by elements of the F, G, and D helices that bind the substrate and exclude solvent from the hydrophobic active site cavity. The observed regiospecific catalytic activity suggests roles of CYP124 in the physiological oxidation of relevant Mtb methyl-branched lipids. The enzymatic specificity and structures reported here provide a scaffold for the design and testing of specific inhibitors of CYP124.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE CYTOCHROME P450 124435Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 1.14
UniProt
Find proteins for P9WPP3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP3 
Go to UniProtKB:  P9WPP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP3
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 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
VGJ
Query on VGJ

Download Ideal Coordinates CCD File 
C [auth A](3R,7S,11S)-3,7,11,15-tetramethylhexadecanoic acid
C20 H40 O2
RLCKHJSFHOZMDR-GBESFXJTSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.596α = 90
b = 73.4β = 90
c = 109.696γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references, Version format compliance
  • Version 1.2: 2018-02-28
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description