3O52

Structure of the E.coli GDP-mannose hydrolase (yffh) in complex with tartrate

Summary for 3O52

• Entry DOI: 10.2210/pdb3o52/pdb
• Related: 3O61 3O69 3O6Z
• Descriptor: GDP-mannose pyrophosphatase nudK, D(-)-TARTARIC ACID, SODIUM ION, ... (5 entities in total)
• Functional Keywords: nudix, gdp_mannose, hydrolase, biofilm, tartrate, nudix fold, gdp-mannose hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 5
• Total formula weight: 110048.44

Authors

Amzel, L.M.,Gabelli, S.B.,Boto, A.N. (deposition date: 2010-07-27, release date: 2011-05-11, Last modification date: 2023-09-06)

Primary citation

Boto, A.N.,Xu, W.,Jakoncic, J.,Pannuri, A.,Romeo, T.,Bessman, M.J.,Gabelli, S.B.,Amzel, L.M.
Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition.
Proteins, 79:2455-2466, 2011

PubMed Abstract: The Nudix hydrolase superfamily, characterized by the presence of the signature sequence GX(5)EX(7)REUXEEXGU (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.

PubMed: 21638333
DOI: 10.1002/prot.23069

Experimental method

X-RAY DIFFRACTION (2.5 Å)