Protein Family Models

haloacid dehalogenase (HAD) family hydrolase uses a nucleophilic aspartate in the phosphoryl transfer reaction; the HAD family includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates

Date:

2024-05-13

This HMM represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs [PMID:7966317]. The subfamilies are defined [PMID:11601995] based on the location and the observed or predicted fold of a so-called "capping domain" [PMID:10956028], or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions.

Date:

2021-04-27

This HMM represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs (PMID:7966317). HAD subfamilies are defined (PMID:11601995) based on the location and the observed or predicted fold of a so-called "capping domain" (PMID:10956028), or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. This model represents variant 3 of subfamily IA, in which the HAD superfamily's third catalytic motif takes the form hhhhDDxxx(x)s, where _s_ refers to a small amino acid and _h_ to a hydrophobic one.

Date:

2021-04-27