Skip to main content

Table 1 Summary of gold standard superfamilies

From: A gold standard set of mechanistically diverse enzyme 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
  1. *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.