4YF5

Crystal structure of Rv1284 in the presence of polycarpine at acidic pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Chemical probing suggests redox-regulation of the carbonic anhydrase activity of mycobacterial Rv1284.

Nienaber, L.Cave-Freeman, E.Cross, M.Mason, L.Bailey, U.M.Amani, P.A Davis, R.Taylor, P.Hofmann, A.

(2015) FEBS J 282: 2708-2721

  • DOI: 10.1111/febs.13313
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The mycobacterial enzyme Rv1284 is a member of the β-carbonic anhydrase family that is considered essential for survival of the pathogen. The active site cavity of this dimeric protein is characterized by an exceptionally small volume and harbours a ...

    The mycobacterial enzyme Rv1284 is a member of the β-carbonic anhydrase family that is considered essential for survival of the pathogen. The active site cavity of this dimeric protein is characterized by an exceptionally small volume and harbours a catalytic zinc ion coordinated by two cysteine and one histidine residue side chains. Using the natural products polycarpine and emodin as chemical probes in crystallographic experiments and stopped-flow enzyme assays, we report that the catalytic activity can be reversibly inhibited by oxidation. Oxidative conditions lead to the removal of one of the active site cysteine residues from the coordination sphere of the catalytic metal ion by engagement in a disulfide bond with another cysteine residue close by. The subsequent loss of the metal ion, which is supported by crystallographic analysis, may thus render the protein catalytically inactive. The oxidative inhibition of Rv1284 can be reversed by exposing the protein to reducing conditions. Because the physical size of the chemical probes used in the present study substantially exceeds the active site volume, we hypothesized that these compounds exert their effects from a surface-bound location and identified Tyr120 as a critical residue for oxidative inactivation. These findings link conditions of oxidative stress to pH homeostasis of the pathogen. Because oxidative stress and acidification are defence mechanisms employed by the innate immune system of the host, we suggest that Rv1284 may be a component of the mycobacterial survival strategy.


    Organizational Affiliation

    Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-carbonic anhydrase 1A, B, C, D172Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: mtcA1canAMT1322
EC: 4.2.1.1
Find proteins for P9WPJ6 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore P9WPJ6 
Go to UniProtKB:  P9WPJ6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.289α = 90
b = 153.932β = 90
c = 159.098γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-02-25 
  • Released Date: 2015-05-06 
  • Deposition Author(s): Hofmann, A.

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2015-07-22
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Data collection, Derived calculations, Refinement description, Source and taxonomy