2WUG

Crystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis in complex with HOPDA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.167 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.170 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HPKClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Characterization of a C-C Hydrolase from Mycobacterium Tuberuclosis Involved in Cholesterol Metabolism.

Lack, N.A.Yam, K.C.Lowe, E.D.Horsman, G.P.Owen, R.L.Sim, E.Eltis, L.D.

(2010) J Biol Chem 285: 434

  • DOI: https://doi.org/10.1074/jbc.M109.058081
  • Primary Citation of Related Structures:  
    2WUD, 2WUE, 2WUF, 2WUG

  • PubMed Abstract: 

    In the recently identified cholesterol catabolic pathway of Mycobacterium tuberculosis, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (HsaD) is proposed to catalyze the hydrolysis of a carbon-carbon bond in 4,5-9,10-diseco-3-hydroxy-5,9,17-tri-oxoandrosta-1(10),2-diene-4-oic acid (DSHA), the cholesterol meta-cleavage product (MCP) and has been implicated in the intracellular survival of the pathogen. Herein, purified HsaD demonstrated 4-33 times higher specificity for DSHA (k(cat)/K(m) = 3.3 +/- 0.3 x 10(4) m(-1) s(-1)) than for the biphenyl MCP 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) and the synthetic analogue 8-(2-chlorophenyl)-2-hydroxy-5-methyl-6-oxoocta-2,4-dienoic acid (HOPODA), respectively. The S114A variant of HsaD, in which the active site serine was substituted with alanine, was catalytically impaired and bound DSHA with a K(d) of 51 +/- 2 mum. The S114A.DSHA species absorbed maximally at 456 nm, 60 nm red-shifted versus the DSHA enolate. Crystal structures of the variant in complex with HOPDA, HOPODA, or DSHA to 1.8-1.9 Aindicate that this shift is due to the enzyme-induced strain of the enolate. These data indicate that the catalytic serine catalyzes tautomerization. A second role for this residue is suggested by a solvent molecule whose position in all structures is consistent with its activation by the serine for the nucleophilic attack of the substrate. Finally, the alpha-helical lid covering the active site displayed a ligand-dependent conformational change involving differences in side chain carbon positions of up to 6.7 A, supporting a two-conformation enzymatic mechanism. Overall, these results provide novel insights into the determinants of specificity in a mycobacterial cholesterol-degrading enzyme as well as into the mechanism of MCP hydrolases.


  • Organizational Affiliation

    Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
A, B
291Mycobacterium tuberculosis H37RvMutation(s): 1 
EC: 3.7.1.8 (PDB Primary Data), 3.7.1.17 (UniProt)
UniProt
Find proteins for P9WNH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNH5 
Go to UniProtKB:  P9WNH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNH5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.167 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.170 (DCC) 
Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.883α = 90
b = 117.971β = 90
c = 180.893γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HPKClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description