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221  structures 4356  species 1  interaction 20961  sequences 63  architectures

Family: Hydrolase_3 (PF08282)

Summary: haloacid dehalogenase-like hydrolase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Haloacid dehydrogenase superfamily". More...

Haloacid dehydrogenase superfamily Edit Wikipedia article

Hydrolase_3
PDB 1rkq EBI.jpg
crystal structure of had-like phosphatase yida from e. coli
Identifiers
Symbol Hydrolase_3
Pfam PF08282
Pfam clan CL0137
InterPro IPR013200

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.[1]

Examples[edit]

A HAD domain is found in several distinct enzymes including:

Human genes encoding proteins that contain this domain include:

References[edit]

  1. ^ 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. 
  2. ^ 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. PMC 102229. PMID 11148289. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ 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. 

This article incorporates text from the public domain Pfam and InterPro IPR013200

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

haloacid dehalogenase-like hydrolase Provide feedback

This family contains haloacid dehalogenase-like hydrolase enzymes.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013200

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]. This HAD domain is found in several distinct enzymes including:

  • Phospholipid-transporting ATPase 1 (EC), a putative lipid-flipping enzyme involved in cold tolerance in Arabidopsis [PUBMED:11148289]
  • 3-deoxy-D-manno-octulosonate (KDO) 8-phosphate phosphatase (EC), which catalyses the final step in the biosynthesis of KDO - a component of lipopolysaccharide in Gram-negative bacteria [PUBMED:12639950]
  • Mannosyl-3-phosphoglycerate phosphatase (EC), which hydrolyzes mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate [PUBMED:11562374]
  • Phosphoglycolate phopshatase (EC), which catalyses the dephosphorylation of 2-phosphoglycolate [PUBMED:14555659]

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HAD (CL0137), which has the following description:

This clan represents the haloacid dehalogenase (HAD) superfamily that includes a diverse range of enzymes that use an asp carboxylate as a nucleophile [1].

The clan contains the following 21 members:

5_nucleotid Acid_phosphat_B Acid_PPase DUF705 HAD HAD_2 Hydrolase Hydrolase_3 Hydrolase_6 Hydrolase_like Hydrolase_like2 LNS2 NIF NT5C PGP_phosphatase PMM PNK3P Put_Phosphatase S6PP Trehalose_PPase UMPH-1

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(69)
Full
(20961)
Representative proteomes NCBI
(23365)
Meta
(3191)
RP15
(948)
RP35
(1870)
RP55
(2569)
RP75
(3153)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(69)
Full
(20961)
Representative proteomes NCBI
(23365)
Meta
(3191)
RP15
(948)
RP35
(1870)
RP55
(2569)
RP75
(3153)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(69)
Full
(20961)
Representative proteomes NCBI
(23365)
Meta
(3191)
RP15
(948)
RP35
(1870)
RP55
(2569)
RP75
(3153)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_66 (Release 17.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 69
Number in full: 20961
Average length of the domain: 223.30 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 85.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 254
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There is 1 interaction for this family. More...

Hydrolase_3

Structures

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 221 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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