1RYA

Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG

Summary for 1RYA

• Entry DOI: 10.2210/pdb1rya/pdb
• Descriptor: GDP-mannose mannosyl hydrolase, MAGNESIUM ION, GUANOSINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: gdp-mannose, mannose, gdp-glucose, nudix, nudix mg-complex, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 38064.01

Authors

Gabelli, S.B.,Bianchet, M.A.,Legler, P.M.,Mildvan, A.S.,Amzel, L.M. (deposition date: 2003-12-20, release date: 2004-06-22, Last modification date: 2024-02-14)

Primary citation

Gabelli, S.B.,Bianchet, M.A.,Azurmendi, H.F.,Xia, Z.,Sarawat, V.,Mildvan, A.S.,Amzel, L.M.
Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus.
Structure, 12:927-935, 2004

PubMed Abstract: GDP-mannose glycosyl hydrolase (GDPMH) catalyzes the hydrolysis of GDP-mannose and GDP-glucose to GDP and sugar by substitution with inversion at C1 of the sugar. The enzyme has a modified Nudix motif and requires one divalent cation for activity. The 1.3 A X-ray structure of the GDPMH-Mg(2+)-GDP complex, together with kinetic, mutational, and NMR data, suggests a mechanism for the GDPMH reaction. Several residues and the divalent cation strongly promote the departure of the GDP leaving group, supporting a dissociative mechanism. Comparison of the GDPMH structure with that of a typical Nudix hydrolase suggests how sequence changes result in the switch of catalytic activity from P-O bond cleavage to C-O bond cleavage. Changes in the Nudix motif result in loss of binding of at least one Mg(2+) ion, and shortening of a loop by 6 residues shifts the catalytic base by approximately 10 A.

PubMed: 15274914
DOI: 10.1016/j.str.2004.03.028

Experimental method

X-RAY DIFFRACTION (1.3 Å)