5DJH

Structure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO4, and 3Mg bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

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This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of Mycobacterium tuberculosis CysQ, with Substrate and Products Bound.

Erickson, A.I.Sarsam, R.D.Fisher, A.J.

(2015) Biochemistry 54: 6830-6841

  • DOI: https://doi.org/10.1021/acs.biochem.5b01000
  • Primary Citation of Related Structures:  
    5DJF, 5DJG, 5DJH, 5DJI, 5DJJ, 5DJK

  • PubMed Abstract: 

    In many organisms, 3'-phosphoadenosine 5'-phosphate (PAP) is a product of two reactions in the sulfur activation pathway. The sulfurylation of biomolecules, catalyzed by sulfotransferases, uses 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfate donor, producing the sulfated biomolecule and PAP product. Additionally, the first step in sulfate reduction for many bacteria and fungi reduces the sulfate moiety of PAPS, producing PAP and sulfite, which is subsequently reduced to sulfide. PAP is removed by the phosphatase activity of CysQ, a 3',5'-bisphosphate nucleotidase, yielding AMP and phosphate. Because excess PAP alters the equilibrium of the sulfur pathway and inhibits sulfotransferases, PAP concentrations can affect the levels of sulfur-containing metabolites. Therefore, CysQ, a divalent cation metal-dependent phosphatase, is a major regulator of this pathway. CysQ (Rv2131c) from Mycobacterium tuberculosis (Mtb) was successfully expressed, purified, and crystallized in a variety of ligand-bound states. Here we report six crystal structures of Mtb CysQ, including a ligand-free structure, a lithium-inhibited state with substrate PAP bound, and a product-bound complex with AMP, phosphate, and three Mg(2+) ions bound. Comparison of these structures together with homologues of the superfamily has provided insight into substrate specificity, metal coordination, and catalytic mechanism.


  • Organizational Affiliation

    Department of Chemistry, ‡Department of Molecular and Cellular Biology, and §Graduate Program in Biochemistry and Molecular, Cellular and Developmental Biology, University of California , One Shields Avenue, Davis, California 95616, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3'-phosphoadenosine 5'-phosphate phosphatase288Mycobacterium tuberculosisMutation(s): 0 
Gene Names: cysQMT2189
EC: 3.1.3.7 (PDB Primary Data), 3.1.3.11 (PDB Primary Data), 3.1.3.25 (PDB Primary Data)
UniProt
Find proteins for P9WKJ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKJ1 
Go to UniProtKB:  P9WKJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKJ1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.636α = 90
b = 58.14β = 90
c = 101.198γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description