1H5Z | pdb_00001h5z

CYTOCHROME P450 14 ALPHA-STEROL DEMETHYLASE (CYP51) FROM MYCOBACTERIUM TUBERCULOSIS IN FERRIC LOW-SPIN STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.236 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Estriol Bound and Ligand-Free Structures of Sterol 14Alpha-Demethylase.

Podust, L.M.Yermalitskaya, L.V.Lepesheva, G.I.Podust, V.N.Dalmasso, E.A.Waterman, M.R.

(2004) Structure 12: 1937

  • DOI: https://doi.org/10.1016/j.str.2004.08.009
  • Primary Citation Related Structures: 
    1H5Z, 1X8V

  • PubMed Abstract: 

    Sterol 14alpha-demethylases (CYP51) are essential enzymes in sterol biosynthesis in eukaryotes and drug targets in antifungal therapy. Here, we report CYP51 structures in ligand-free and estriol bound forms. Using estriol as a probe, we determined orientation of the substrate in the active site, elucidated protein contacts with the invariant 3beta-hydroxy group of a sterol, and identified F78 as a key discriminator between 4alpha-methylated and 4alpha,beta-dimethylated substrates. Analysis of CYP51 dynamics revealed that the C helix undergoes helix-coil transition upon binding and dissociation of a ligand. Loss of helical structure of the C helix in the ligand-free form results in an unprecedented opening of the substrate binding site. Upon binding of estriol, the BC loop loses contacts with molecular surface and tends to adopt a closed conformation. A mechanism for azole resistance in the yeast pathogen Candida albicans associated with mutations in the ERG11 gene encoding CYP51 is suggested based on CYP51 protein dynamics.


  • Organizational Affiliation
    • Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. larissa.m.podust@vanderbilt.edu

Macromolecule Content 

  • Total Structure Weight: 52.17 kDa 
  • Atom Count: 3,761 
  • Modeled Residue Count: 435 
  • Deposited Residue Count: 455 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYTOCHROME P450 51455Mycobacterium tuberculosisMutation(s): 0 
Gene Names: CYP51RV0764CMTCY369.09C
EC: 1.14.13.70 (PDB Primary Data), 1.14.15.36 (UniProt)
UniProt
Find proteins for P9WPP9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP9 
Go to UniProtKB:  P9WPP9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP9
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.236 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.489α = 90
b = 84.827β = 90
c = 110.025γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-03
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2015-08-05
    Changes: Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description