Summary: haloacid dehalogenase-like hydrolase
This is the Wikipedia entry entitled "Haloacid dehydrogenase superfamily". More...
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Haloacid dehydrogenase superfamily Edit Wikipedia article
crystal structure of had-like phosphatase yida from e. coli
In molecular biology, the haloacid dehydrogenase superfamily (HAD superfamily) includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification.
- Phospholipid-translocating ATPase EC 220.127.116.11, a putative lipid-flipping enzyme involved in cold tolerance in Arabidopsis 
- 3-deoxy-D-manno-octulosonate (KDO) 8-phosphate phosphatase (EC 18.104.22.168), which catalyses the final step in the biosynthesis of KDO - a component of lipopolysaccharide in Gram-negative bacteria
- Mannosyl-3-phosphoglycerate phosphatase (EC 22.214.171.124), which hydrolyses mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate
- Phosphoglycolate phosphatase (EC 126.96.36.199), which catalyses the dephosphorylation of 2-phosphoglycolate
Human genes encoding proteins that contain this domain include:
- Koonin EV, Tatusov RL (November 1994). "Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search". J. Mol. Biol. 244 (1): 125–32. doi:10.1006/jmbi.1994.1711. PMID 7966317.
- Gomes E, Jakobsen MK, Axelsen KB, Geisler M, Palmgren MG (December 2000). "Chilling tolerance in Arabidopsis involves ALA1, a member of a new family of putative aminophospholipid translocases". Plant Cell 12 (12): 2441–2454. doi:10.2307/3871240. PMC 102229. PMID 11148289.
- Wu J, Woodard RW (May 2003). "Escherichia coli YrbI is 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase". J. Biol. Chem. 278 (20): 18117–23. doi:10.1074/jbc.M301983200. PMID 12639950.
- Empadinhas N, Marugg JD, Borges N, Santos H, da Costa MS (November 2001). "Pathway for the synthesis of mannosylglycerate in the hyperthermophilic archaeon Pyrococcus horikoshii. Biochemical and genetic characterization of key enzymes". J. Biol. Chem. 276 (47): 43580–8. doi:10.1074/jbc.M108054200. PMID 11562374.
- Kim Y, Yakunin AF, Kuznetsova E, Xu X, Pennycooke M, Gu J, Cheung F, Proudfoot M, Arrowsmith CH, Joachimiak A, Edwards AM, Christendat D (January 2004). "Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum". J. Biol. Chem. 279 (1): 517–26. doi:10.1074/jbc.M306054200. PMC 2795321. PMID 14555659.
haloacid dehalogenase-like hydrolase Provide feedback
This family contains haloacid dehalogenase-like hydrolase enzymes.
Internal database links
|SCOOP:||PNK3P DUF2608 Acid_PPase HAD Hydrolase_6 HAD_2 DUF4392|
|Similarity to PfamA using HHSearch:||Hydrolase Trehalose_PPase PMM Acid_phosphat_B S6PP Hydrolase_6 HAD_2|
This tab holds annotation information from the InterPro database.
InterPro entry IPR023214
The haloacid dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification[PUBMED:7966317].
Crystal structures of proteins from the HAD superfamily show that these proteins all share a conserved alpha/beta-domain classified as a hydrolase fold, which is similar to the Rossmann fold [PUBMED:14555659]. This conserved domain usually contains an insertion (sub)domain. For example, the crystal structure of a phosphoglycolate phosphatase from Thermoplasma acidophilum [PUBMED:14555659] revealed two distinct domains, a larger core domain and a smaller cap domain. The large domain is composed of a centrally located five-stranded parallel beta-sheet with strand order S10, S9, S8, S1, S2 and a small beta-hairpin, strands S3 andS4. This central sheet is flanked by a set of three aplha-helices on one side and two helices on the other. The topology of the large domain is conserved; however, structural variation is observed in the smaller domain among the different functional classes of the haloacid dehalogenase superfamily.
This entry represents the large domain with conserved topology among the HAD superfamily.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This clan represents the haloacid dehalogenase (HAD) superfamily that includes a diverse range of enzymes that use an asp carboxylate as a nucleophile .
The clan contains the following 22 members:5_nucleotid Acid_phosphat_B Acid_PPase Cation_ATPase DUF2608 DUF705 HAD HAD_2 Hydrolase Hydrolase_3 Hydrolase_6 Hydrolase_like LNS2 NIF NT5C PGP_phosphatase PMM PNK3P Put_Phosphatase S6PP Trehalose_PPase UMPH-1
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
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- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Pfam-B_66 (Release 17.0)|
|Number in seed:||66|
|Number in full:||5547|
|Average length of the domain:||208.40 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||77.05 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Hydrolase_3 domain has been found. There are 264 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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