4G63 image
Deposition Date 2012-07-18
Release Date 2012-10-10
Last Version Date 2023-09-13
Entry Detail
PDB ID:
4G63
Title:
Crystal structure of cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) in complex with phosphate ions from Legionella pneumophila, Northeast Structural Genomics Consortium Target LgR1
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.70 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
I 41 2 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytosolic IMP-GMP specific 5'-nucleotidase
Gene (Uniprot):lpg0095
Chain IDs:A
Chain Length:470
Number of Molecules:1
Biological Source:Legionella pneumophila subsp. pneumophila
Ligand Molecules
Primary Citation
Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila.
Febs J. 281 1613 1628 (2014)
PMID: 24456211 DOI: 10.1111/febs.12727

Abstact

UNLABELLED Cytosolic nucleotidase II (cN-II) from Legionella pneumophila (Lp) catalyzes the hydrolysis of GMP and dGMP displaying sigmoidal curves, whereas catalysis of IMP hydrolysis displayed a biphasic curve in the initial rate versus substrate concentration plots. Allosteric modulators of mammalian cN-II did not activate LpcN-II although GTP, GDP and the substrate GMP were specific activators. Crystal structures of the tetrameric LpcN-II revealed an activator-binding site at the dimer interface. A double mutation in this allosteric-binding site abolished activation, confirming the structural observations. The substrate GMP acting as an activator, partitioning between the allosteric and active site, is the basis for the sigmoidicity of the initial velocity versus GMP concentration plot. The LpcN-II tetramer showed differences in subunit organization upon activator binding that are absent in the activator-bound human cN-II structure. This is the first observation of a structural change induced by activator binding in cN-II that may be the molecular mechanism for enzyme activation. DATABASE The coordinates and structure factors reported in this paper have been submitted to the Protein Data Bank under the accession numbers 2BDE and 4G63. The accession number of GMP complexed LpcN-II is 4OHF. STRUCTURED DIGITAL ABSTRACT LpcN-II and LpcN-II bind by molecular sieving (View interaction) LpcN-II and LpcN-II bind by x-ray crystallography (View interaction) [Structured digital abstract was added on 5 March 2014 after original online publication].

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