Pathways & interactions
HAD-superfamily hydrolase, subfamily IIA (IPR006357)
Short name: HAD-SF_hydro_IIA
Overlapping homologous superfamilies
- HAD-like superfamily (IPR036412)
- HAD-superfamily hydrolase, subfamily IIA (IPR006357)
- 2-phosphoglycolate phosphatase, eukaryotic (IPR006349)
- HAD hydrolase, LHPP/HDHD2 (IPR006355)
- HAD-superfamily hydrolase, subfamily IIA, CECR5 (IPR006353)
- HAD-superfamily hydrolase, subfamily IIA, hypothetical 1 (IPR006354)
- HAD-superfamily hydrolase, subfamily IIA, hypothetical 3 (IPR006356)
These sequences form one of the structural subclasses 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 classes 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. Class I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Class II consists of sequences in which the capping domain is found between the second and third motifs. Class III sequences have no capping domain in either of these positions. The Class IIA capping domain is predicted to consist of a mixed alpha-beta fold with the basic pattern: Helix-Helix-Helix-Sheet-Helix-Loop-Sheet-Helix-Sheet-Helix. Presently, this subfamily covers the eukaryotic phosphoglycolate phosphatase, as well as four further subfamilies covering closely related sequences in eukaryotes, in Gram-positive bacteria and in Gram-negative bacteria. The Escherichia coli NagD gene and the Bacillus subtilis AraL gene are members of this subfamily but are not members of the any of the presently defined equivalogs within it. NagD is part of the NAG operon responsible for N-acetylglucosamine metabolism [PMID: 2190615]. Genes from several organisms have been annotated as NagD, or NagD-like. However, without data on the presence of other members of this pathway, (such as in the case of Yersinia pestis) these assignments should not be given great weight. The AraL gene is similar and is part of the L-arabinose operon [PMID: 9084180]. A gene from Halobacterium has been annotated as AraL, but no other Ara operon genes have been annotated. Many of the genes in this subfamily have been annotated as "pNPPase" "4-nitrophenyl phosphatase" or "NPPase". These all refer to the same activity versus a common lab test compound used to determine phosphatase activity. There is no evidence that this activity is physiologically relevant. Dihydroxyacetone phosphatase from Corynebacterium glutamicum is also a member of this superfamily, and catalyzes the dephosphorylation of dihydroxyacetone phosphate to produce 1,3-dihydroxyacetone [PMID: 23108048].
The structure of NagD from Escherichia coli> (strain K12) has been reported and its activity against various substrates determined. It has high specificity for nucleotide monophosphates, and in particular UMP and GMP. In the context of its occurrence in the NAG operon, it may well be involved in the recycling of cell wall metabolites [PMID: 16430214].