5DJI

Structure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO4, and 2Mg bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.659 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/acs.biochem.5b01000
  • Primary Citation of Related Structures:  

  • 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 sulfat ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3'-phosphoadenosine 5'-phosphate phosphatase
A
288Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: cysQ
EC: 3.1.3.7
Find proteins for P9WKJ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WKJ1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.659 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.637α = 90.00
b = 58.200β = 90.00
c = 101.510γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-02
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Refinement description