7EF6

Crystal Structure of Xanthosine monophosphate phosphatase in the unliganded state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Initiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase.

Heinemann, K.J.Yang, S.Y.Straube, H.Medina-Escobar, N.Varbanova-Herde, M.Herde, M.Rhee, S.Witte, C.P.

(2021) Nat Commun 12: 6846-6846

  • DOI: https://doi.org/10.1038/s41467-021-27152-4
  • Primary Citation of Related Structures:  
    7EF6, 7EF7

  • PubMed Abstract: 

    In plants, guanosine monophosphate (GMP) is synthesized from adenosine monophosphate via inosine monophosphate and xanthosine monophosphate (XMP) in the cytosol. It has been shown recently that the catabolic route for adenylate-derived nucleotides bifurcates at XMP from this biosynthetic route. Dephosphorylation of XMP and GMP by as yet unknown phosphatases can initiate cytosolic purine nucleotide catabolism. Here we show that Arabidopsis thaliana possesses a highly XMP-specific phosphatase (XMPP) which is conserved in vascular plants. We demonstrate that XMPP catalyzes the irreversible entry reaction of adenylate-derived nucleotides into purine nucleotide catabolism in vivo, whereas the guanylates enter catabolism via an unidentified GMP phosphatase and guanosine deaminase which are important to maintain purine nucleotide homeostasis. We also present a crystal structure and mutational analysis of XMPP providing a rationale for its exceptionally high substrate specificity, which is likely required for the efficient catalysis of the very small XMP pool in vivo.


  • Organizational Affiliation

    Leibniz Universität Hannover, Department of Molecular Nutrition and Biochemistry of Plants, Herrenhäuser Strasse 2, 30419, Hannover, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xanthosine monophosphate phosphatase250Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g32150At2g32150/F22D22.10F22D22.10F22D22_10
UniProt
Find proteins for Q9SKY5 (Arabidopsis thaliana)
Explore Q9SKY5 
Go to UniProtKB:  Q9SKY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SKY5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.063α = 90
b = 55.276β = 93.862
c = 57.154γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description