7EF6 image
Deposition Date 2021-03-21
Release Date 2021-11-03
Last Version Date 2023-11-29
Entry Detail
PDB ID:
7EF6
Keywords:
Title:
Crystal Structure of Xanthosine monophosphate phosphatase in the unliganded state
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.34 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Xanthosine monophosphate phosphatase
Gene (Uniprot):F22D22.10, F22D22_10
Chain IDs:A
Chain Length:250
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Ligand Molecules
Primary Citation
Initiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase.
Nat Commun 12 6846 6846 (2021)
PMID: 34824243 DOI: 10.1038/s41467-021-27152-4

Abstact

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.

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