Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition

Agedi N. Boto, Wenlian Xu, Jean Jakoncic, Archana Pannuri, Tony Romeo, Maurice J. Bessman, Sandra B. Gabelli, L. Mario Amzel

Research output: Contribution to journalArticlepeer-review

Abstract

The Nudix hydrolase superfamily, characterized by the presence of the signature sequence GX 5EX 7REUXEEXGU (where U is I, L, or V), is a well-studied family in which relations have been established between primary sequence and substrate specificity for many members. For example, enzymes that hydrolyze the diphosphate linkage of ADP-ribose are characterized by having a proline 15 amino acids C-terminal of the Nudix signature sequence. GDPMK is a Nudix enzyme that conserves this characteristic proline but uses GDP-mannose as the preferred substrate. By investigating the structure of the GDPMK alone, bound to magnesium, and bound to substrate, the structural basis for this divergent substrate specificity and a new rule was identified by which ADP-ribose pyrophosphatases can be distinguished from purine-DP-mannose pyrophosphatases from primary sequence alone. Kinetic and mutagenesis studies showed that GDPMK hydrolysis does not rely on a single glutamate as the catalytic base. Instead, catalysis is dependent on residues that coordinate the magnesium ions and residues that position the substrate properly for catalysis. GDPMK was thought to play a role in biofilm formation because of its upregulation in response to RcsC signaling; however, GDPMK knockout strains show no defect in their capacity of forming biofilms.

Original languageEnglish (US)
Pages (from-to)2455-2466
Number of pages12
JournalProteins: Structure, Function and Bioinformatics
Volume79
Issue number8
DOIs
StatePublished - Aug 2011

Keywords

  • ADP-ribose hydrolase
  • Biofilm
  • GDP-mannose hydrolase
  • Markless knockout
  • Nudix
  • YffH

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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