PDBsum entry 1wcq

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Hydrolase PDB id
Protein chains
601 a.a.
GOL ×7
DAN ×3
_NA ×3
Waters ×1078

References listed in PDB file
Key reference
Title Two nucleophilic mutants of the micromonospora viridifaciens sialidase operate with retention of configuration by two different mechanisms.
Authors J.N.Watson, S.Newstead, A.A.Narine, G.Taylor, A.J.Bennet.
Ref. Chembiochem, 2005, 6, 1999-2004. [DOI no: 10.1002/cbic.200500114]
PubMed id 16206228
Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.
Mutants of the Micromonospora viridifaciens sialidase, Y370E and Y370F, are catalytically active retaining enzymes that operate by different mechanisms. Previous substitutions with smaller amino acids, including Y370D, yielded inverting sialidases. At least one water molecule can fit into the active-site cavity of this mutant and act as a nucleophile from the face opposite the leaving group (Biochemistry 2003, 42, 12 682). Thus, addition of a CH(2) unit (Asp versus Glu) changes the mechanism from inversion back to retention of configuration. Based on Brønsted beta(lg) values, it is proposed that the Y370E mutant reacts by a double-displacement mechanism (beta(lg) on k(cat)/K(m) -0.36+/-0.04) with Glu370 acting as the nucleophile. However, the Y370F mutant (beta(lg) on k(cat)/K(m) -0.79+/-0.12) reacts via a dissociative transition state. The crystal structure of the Y370F mutant complexed with 2-deoxy-2,3-dehydro-N-acetylneuraminic acid shows no significant active-site perturbation relative to the wild-type enzyme.
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