Crystal structure of E. coli PRPP synthetase

Weijie Zhou, Andrew Tsai, Devon A. Dattmore, Devin P. Stives, Iva Chitrakar, Alexis M. D'Alessandro, Shiv Patil, Katherine A. Hicks, Jarrod B. French

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Background: Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) is an enzyme that catalyzes the ATP-dependent conversion of ribose-5-phosphate to phosphoribosyl pyrophosphate. The reaction product is a key precursor for the biosynthesis of purine and pyrimidine nucleotides. Results: We report the 2.2 Å crystal structure of the E. coli ribose-phosphate pyrophosphobinase (EcKPRS). The protein has two type I phosphoribosyltransferase folds, related by 2-fold pseudosymmetry. The propeller-shaped homohexameric structure of KPRS is composed of a trimer of dimers, with the C-terminal domains forming the dimeric blades of the propeller and the N-terminal domains forming the hexameric core. The key, conserved active site residues are well-defined in the structure and positioned appropriately to bind substrates, adenosine monophosphate and ribose-5-phosphate. The allosteric site is also relatively well conserved but, in the EcKPRS structure, several residues from a flexible loop occupy the site where the allosteric modulator, adenosine diphosphate, is predicted to bind. The presence of the loop in the allosteric site may be an additional level of regulation, whereby low affinity molecules are precluded from binding. Conclusions: Overall, this study details key structural features of an enzyme that catalyzes a critical step in nucleotide metabolism. This work provides a framework for future studies of this important protein and, as nucleotides are critical for viability, may serve as a foundation for the development of novel anti-bacterial drugs.

Original languageEnglish (US)
Article number1
JournalBMC Structural Biology
Volume19
Issue number1
DOIs
StatePublished - Jan 15 2019
Externally publishedYes

Bibliographical note

Funding Information:
JBF would like to acknowledge support from the National Science Foundation, award numbers 1455596 and 1750637, and the National Institutes of General Medical Sciences of the National Institutes of Health under Grant R35GM124898. This work is based upon research conducted at the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P41 GM103403). The Pilatus 6 M detector on 24-ID-C beam line is funded by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. The funding bodies were not involved in the design of the study, the collection, analysis or interpretation of the data, or writing the manuscript.

Publisher Copyright:
© 2019 The Author(s).

Keywords

  • KPRS
  • Nucleotide biosynthesis
  • Phosphoribosyl pyrophosphate
  • Purines
  • Pyrimidines
  • Ribose-5-phosphate

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