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305  structures 4889  species 5  interactions 29620  sequences 255  architectures

Family: His_Phos_1 (PF00300)

Summary: Histidine phosphatase superfamily (branch 1)

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 "Phosphatase". More...

Phosphatase Edit Wikipedia article

A ball and stick model of a phosphate anion.

A phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol. Because a phosphatase enzyme catalyzes the hydrolysis of its substrate, it is a subcategory of hydrolases.[1] Phosphatase enzymes are essential to many biological functions, because phosphorylation (e.g. by protein kinases) and dephosphorylation serve diverse roles in cellular regulation and signaling.[2] Whereas phosphatases remove phosphate groups from molecules, kinases catalyze the transfer of phosphate groups to molecules from ATP. Together, kinases and phosphatases direct a form of post-translational modification that is essential to the cell’s regulatory network.[3] Phosphatase enzymes are not to be confused with phosphorylase enzymes, which catalyze the transfer of a phosphate group from hydrogen phosphate to an acceptor. Due to their prevalence in cellular regulation, phosphatases are an area of interest for pharmaceutical research.[4][5]

Biochemistry

The general reaction catalyzed by a phosphatase enzyme

Phosphatases catalyze the hydrolysis of a phosphomonoester, removing a phosphate moiety from the substrate. Water is split in the reaction, with the -OH group attaching to the phosphate ion, and the H+ protonating the hydroxyl group of the other product. The net result of the reaction is the destruction of a phosphomonoester and the creation of both a phosphate ion and a molecule with a free hydroxyl group.[4]

Phosphatases are able to dephosphorylate seemingly different sites on their substrates with great specificity. Identifying the "phosphatase code," that is, the mechanisms and rules that govern substrate recognition for phosphatases, is still a work in progress, although the first comparative analysis of all the protein phosphatases encoded across nine eucaryotic 'phosphatome' genomes is now available.[6] Studies reveal that so called "docking interactions" play a significant role in substrate binding.[3] A phosphatase recognizes and interacts with various motifs (elements of secondary structure) on its substrate; these motifs bind with low affinity to docking sites on the phosphatase, which are not contained within its active site. Although each individual docking interaction is weak, many interactions occur simultaneously, conferring a cumulative effect on binding specificity.[7] Docking interactions can also allosterically regulate phosphatases and thus influence their catalytic activity.[8]

Functions

In contrast to kinases, phosphatase enzymes recognize and catalyze a wider array of substrates and reactions. For example, in humans, Ser/Thr kinases outnumber Ser/Thr phosphatases by a factor of ten.[4] To some extent, this disparity results from incomplete knowledge of the human phosphatome, that is, the complete set of phosphatases expressed in a cell, tissue, or organism.[3] Many phosphatases have yet to be discovered, and for numerous known phosphatases, a substrate has yet to be identified. However, among well-studied phosphatase/kinase pairs, phosphatases exhibit greater variety than their kinase counterparts in both form and function; this may result from the lesser degree of conservation among phosphatases.[4]

Calcineurin (PP2B) is a protein phosphatase enzyme involved in immune system function.

Protein phosphatases

Main article: Protein phosphatase

A protein phosphatase is an enzyme that dephosphorylates an amino acid residue of its protein substrate. Whereas protein kinases act as signaling molecules by phosphorylating proteins, phosphatases remove the phosphate group, which is essential if the system of intracellular signaling is to be able to reset for future use. The tandem work of kinases and phosphatases constitute a significant element of the cell’s regulatory network.[9] Phosphorylation (and dephosphorylation) is among the most common modes of posttranslational modification in proteins, and it is estimated that, at any given time, up to 30% of all proteins are phosphorylated.[10][11] Two notable protein phosphatases are PP2A and PP2B. PP2A is involved in multiple regulatory processes, such as DNA replication, metabolism, transcription, and development. PP2B, also called calcineurin, is involved in the proliferation of T cells; because of this, it is the target of some drugs that seek to suppress the immune system.[9]

Nucleosides and nucleotides differ by one phosphate, which is cleaved from nucleotides by nucleotidases.

Nucleotidases

Main article: Nucleotidase

A nucleotidase is an enzyme that catalyzes the hydrolysis of a nucleotide, forming a nucleoside and a phosphate ion.[12] Nucleotidases are essential for cellular homeostasis, because they are partially responsible for maintaining a balanced ratio of nucleotides to nucleosides.[13] Some nucleotidases function outside the cell, creating nucleosides that can be transported into the cell and used to regenerate nucleotides via salvage pathways.[14] Inside the cell, nucleotidases may help to maintain energy levels under stress conditions. A cell deprived of oxygen and nutrients may catabolize more nucleotides to boost levels of nucleoside triphosphates such as ATP, the primary energy currency of the cell.[15]

In gluconeogenesis

Phosphatases can also act on carbohydrates, such as intermediates in gluconeogenesis. Gluconeogenesis is a biosynthetic pathway wherein glucose is created from noncarbohydrate precursors; the pathway is essential because many tissues can only derive energy from glucose.[9] Two phosphatases, glucose-6-phosphatase and fructose-1,6-bisphosphatase, catalyze irreversibe steps in gluconeogenesis.[16][17] Each cleaves a phosphate group from a six-carbon sugar phosphate intermediate.

Classification

Within the larger class of phosphatase, the Enzyme Commission recognizes 104 distinct enzyme families. Phosphatases are classified by substrate specificity and sequence homology in catalytic domains.[3] Despite their classification into over one hundred families, all phosphatases still catalyze the same general hydrolysis reaction.[1]

In some ways, phosphatase enzymes defy the currently-accepted classification system. It is not the case that one phosphatase enzyme recognizes only one substrate. On the contrary, they are promiscuous enzymes: one phosphatase may recognize many different substrates, and one substrate may be recognized by many different phosphatases.[3] In some cases, a protein phosphatase (i.e. one defined by its recognition of protein substrates) can catalyze the dephosphorylation of nonprotein substrates.[4] Similarly, dual-specificity tyrosine phosphatases can dephosphorylate not only tyrosine residues, but also serine residues. Thus, one phosphatase can exhibit the qualities of multiple phosphatase families.[9]

See also

References

  1. ^ a b "ENZYME: 3.1.3.-". enzyme.expasy.org. Retrieved 2017-02-21. 
  2. ^ Liberti, Susanna; Sacco, Francesca; Calderone, Alberto; Perfetto, Livia; Iannuccelli, Marta; Panni, Simona; Santonico, Elena; Palma, Anita; Nardozza, Aurelio P. (2013-01-01). "HuPho: the human phosphatase portal". FEBS Journal. 280 (2): 379–387. doi:10.1111/j.1742-4658.2012.08712.x. ISSN 1742-4658. 
  3. ^ a b c d e Sacco, Francesca; Perfetto, Livia; Castagnoli, Luisa; Cesareni, Gianni (2012-08-14). "The human phosphatase interactome: An intricate family portrait". Febs Letters. 586 (17): 2732–2739. doi:10.1016/j.febslet.2012.05.008. ISSN 0014-5793. PMC 3437441Freely accessible. PMID 22626554. 
  4. ^ a b c d e Li, Xun; Wilmanns, Matthias; Thornton, Janet; Köhn, Maja (2013-05-14). "Elucidating Human Phosphatase-Substrate Networks". Science Signaling. 6 (275): rs10. doi:10.1126/scisignal.2003203. 
  5. ^ Bodenmiller, Bernd; Wanka, Stefanie; Kraft, Claudine; Urban, Jörg; Campbell, David; Pedrioli, Patrick G.; Gerrits, Bertran; Picotti, Paola; Lam, Henry (2010-12-21). "Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast". Science Signaling. 3 (153): rs4. doi:10.1126/scisignal.2001182. PMC 3072779Freely accessible. PMID 21177495. 
  6. ^ Chen, Mark J.; Dixon, Jack E.; Manning, Gerard (2017-04-11). "Genomics and evolution of protein phosphatases". Sci. Signal. 10 (474): eaag1796. doi:10.1126/scisignal.aag1796. ISSN 1945-0877. PMID 28400531. 
  7. ^ Roy, Jagoree; Cyert, Martha S. (2009-12-08). "Cracking the Phosphatase Code: Docking Interactions Determine Substrate Specificity". Science Signaling. 2 (100): re9. doi:10.1126/scisignal.2100re9. 
  8. ^ Reményi, Attila; Good, Matthew C; Lim, Wendell A (2006-12-01). "Docking interactions in protein kinase and phosphatase networks". Current Opinion in Structural Biology. Catalysis and regulation / Proteins. 16 (6): 676–685. doi:10.1016/j.sbi.2006.10.008. 
  9. ^ a b c d G., Voet, Judith; W., Pratt, Charlotte (2013-01-01). Fundamentals of biochemistry : life at the molecular level. Wiley. ISBN 9781118129180. OCLC 892195795. 
  10. ^ Cohen, Philip (2002-05-01). "The origins of protein phosphorylation". Nature Cell Biology. 4 (5): E127–130. doi:10.1038/ncb0502-e127. ISSN 1465-7392. PMID 11988757. 
  11. ^ Tonks, Nicholas K. "Protein tyrosine phosphatases: from genes, to function, to disease". Nature Reviews Molecular Cell Biology. 7 (11): 833–846. doi:10.1038/nrm2039. 
  12. ^ "ENZYME entry 3.1.3.31". enzyme.expasy.org. Retrieved 2017-03-21. 
  13. ^ Bianchi, V; Pontis, E; Reichard, P (1986). "Interrelations between substrate cycles and de novo synthesis of pyrimidine deoxyribonucleoside triphosphates in 3T6 cells". Proceedings of the National Academy of Sciences of the United States of America. 83: 986–990. PMC 322995Freely accessible. 
  14. ^ Zimmermann, Herbert; Zebisch, Matthias; Sträter, Norbert (2012-09-01). "Cellular function and molecular structure of ecto-nucleotidases". Purinergic Signalling. 8 (3): 437–502. doi:10.1007/s11302-012-9309-4. ISSN 1573-9538. PMC 3360096Freely accessible. PMID 22555564. 
  15. ^ Hunsucker, Sally Anne; Mitchell, Beverly S.; Spychala, Jozef (2005-07-01). "The 5'-nucleotidases as regulators of nucleotide and drug metabolism". Pharmacology & Therapeutics. 107 (1): 1–30. doi:10.1016/j.pharmthera.2005.01.003. ISSN 0163-7258. PMID 15963349. 
  16. ^ "ENZYME entry 3.1.3.9". enzyme.expasy.org. Retrieved 2017-03-21. 
  17. ^ "ENZYME entry 3.1.3.11". enzyme.expasy.org. Retrieved 2017-03-21. 

External links

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.

Histidine phosphatase superfamily (branch 1) Provide feedback

The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches. The larger branch 1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase. The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases. The bacterial regulatory protein phosphatase SixA is also in branch 1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in branch 1 members.

Literature references

  1. Rigden DJ;, Biochem J. 2008;409:333-348.: The histidine phosphatase superfamily: structure and function. PUBMED:18092946 EPMC:18092946


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013078

The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches. The relationship between the two branches is not evident by (PSI-)BLAST but is clear from more sensitive sequence searches and structural comparisons [PUBMED:18092946].

The larger clade-1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase. The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases. The bacterial regulatory protein phosphatase SixA is also in clade-1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in clade-1 members.

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 His_phosphatase (CL0071), which has the following description:

The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches [1].

The clan contains the following 2 members:

His_Phos_1 His_Phos_2

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(375)
Full
(29620)
Representative proteomes UniProt
(76676)
NCBI
(116133)
Meta
(6865)
RP15
(5400)
RP35
(15502)
RP55
(27524)
RP75
(42126)
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  Seed
(375)
Full
(29620)
Representative proteomes UniProt
(76676)
NCBI
(116133)
Meta
(6865)
RP15
(5400)
RP35
(15502)
RP55
(27524)
RP75
(42126)
Alignment:
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  Seed
(375)
Full
(29620)
Representative proteomes UniProt
(76676)
NCBI
(116133)
Meta
(6865)
RP15
(5400)
RP35
(15502)
RP55
(27524)
RP75
(42126)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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.

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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: Prosite
Previous IDs: PGAM;
Type: Domain
Author: Finn RD, Griffiths-Jones SR, Rigden DJ
Number in seed: 375
Number in full: 29620
Average length of the domain: 157.20 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 62.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 194
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 5 interactions for this family. More...

NUDIX 6PF2K 6PF2K His_Phos_1 NUDIX

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 His_Phos_1 domain has been found. There are 305 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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