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J Am Chem Soc. 2016 Nov 16;138(45):15035-15045. Epub 2016 Nov 4.

Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases.

Author information

1
Department of Biotechnology and Food Sciences, Budapest University of Technology and Economics , Budapest 1111, Hungary.
2
Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary.
3
Department of Chemistry, King's College London , London SE1 1DB, United Kingdom.
4
MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary.
5
Core Technologies Centre, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest 1117, Hungary.
6
Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , Rockville, Maryland 10892-9314, United States.

Abstract

Arginine finger is a highly conserved and essential residue in many GTPase and AAA+ ATPase enzymes that completes the active site from a distinct protomer, forming contacts with the γ-phosphate of the nucleotide. To date, no pyrophosphatase has been identified that employs an arginine finger fulfilling all of the above properties; all essential arginine fingers are used to catalyze the cleavage of the γ-phosphate. Here, we identify and unveil the role of a conserved arginine residue in trimeric dUTPases that meets all the criteria established for arginine fingers. We found that the conserved arginine adjacent to the P-loop-like motif enables structural organization of the active site for efficient catalysis via its nucleotide coordination, while its direct electrostatic role in transition state stabilization is secondary. An exhaustive structure-based comparison of analogous, conserved arginines from nucleotide hydrolases and transferases revealed a consensus amino acid location and orientation for contacting the γ-phosphate of the substrate nucleotide. Despite the structurally equivalent position, functional differences between arginine fingers of dUTPases and NTPases are explained on the basis of the unique chemistry performed by the pyrophosphatase dUTPases.

PMID:
27740761
DOI:
10.1021/jacs.6b09012
[Indexed for MEDLINE]
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