Crystal structures identify an atypical two-metal-ion mechanism for uridyltransfer in GlmU: Its significance to sugar nucleotidyl transferases

Pravin Kumar Ankush Jagtap, Sunil Kumar Verma, Neha Vithani, Vaibhav Singh Bais, Balaji Prakash

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Abstract

N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU), exclusive to prokaryotes, is a bifunctional enzyme that synthesizes UDP-GlcNAc - an important component of the cell wall of many microorganisms. Uridyltransfer, one of the reactions it catalyzes, involves binding GlcNAc-1-P, UTP and Mg2 + ions; however, whether one or two ions catalyze this reaction remains ambiguous. Here, we resolve this using biochemical and crystallographic studies on GlmU from Mycobacterium tuberculosis (GlmUMtb) and identify a two-metal-ion mechanism (mechanism-B). In contrast to well-established two-metal mechanism (mechanism-A) for enzymes acting on nucleic acids, mechanism-B is distinct in the way the two Mg2 + ions (Mg2 +A and Mg2 +B) are positioned and stabilized. Further, attempts to delineate the roles of the metal ions in substrate stabilization, nucleophile activation and transition-state stabilization are presented. Interestingly, a detailed analysis of the available structures of sugar nucleotidyl transferases (SNTs) suggests that they too would utilize mechanism-B rather than mechanism-A. Based on this, SNTs could be classified into Group-I, which employs the two-metal mechanism-B as in GlmU, and Group-II that employs a variant one-metal mechanism-B, wherein the role of Mg2 +A is substituted by a conserved lysine. Strikingly, eukaryotic SNTs appear confined to Group-II. Recognizing these differences may be important in the design of selective inhibitors against microbial nucleotidyl transferases.

Original languageEnglish (US)
Pages (from-to)1745-1759
Number of pages15
JournalJournal of Molecular Biology
Volume425
Issue number10
DOIs
StatePublished - May 27 2013

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Keywords

  • catalytic mechanism
  • magnesium ion
  • nucleotidyl transfer reaction
  • pyrophosphorylase
  • structural biology

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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