A gold standard set of mechanistically diverse enzyme superfamilies

Table 1 Summary of gold standard superfamilies

Superfamily	Common chemical capability	Fold*	Number of families	Number of sequences^†	Number of structures^‡
Amidohydrolase	Metal ion(s) deprotonate water for nucleophilic attack on substrate	TIM beta/alpha-barrel	29	905	98
Crotonase	Stabilization of enolate anion intermediate derived from acyl-CoA substrate	ClpP/crotonase	16	970	22
Enolase	Abstraction of proton alpha to carboxylic acid, leading to a stabilized enolate anion intermediate	TIM beta/alpha-barrel	9	1,050	63
Haloacid dehalogenase	Active site Asp forms covalent enzyme-substrate intermediate, facilitating cleavage of C-Cl, P-C or P-O bond	HAD-like	20	1,281	50
Vicinal oxygen chelate	Metal coordination environment promotes direct electrophilic participation of metal in catalysis	Glyoxalase/bleomycin resistance protein/dihydroxybiphenyl dioxygenase	17	681	49

*Fold class, as defined by the Structural Classification of Proteins (SCOP). Note that the gold standard superfamilies are subsets of SCOP fold classes, and thus may not contain all members of their SCOP fold class. ^†The number of sequences listed in this table for a gold standard superfamily may not match the corresponding number in the SFLD because some SFLD sequences are kept private, pending publication of the family into which they have been classified (these sequences appear in the gold standard set without a family classification), or because the SFLD may contain additional sequences obtained during periodic updating. ^‡Includes mutant structures. Multiple structures may correspond to a single sequence.

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