Difference between revisions of "Phosphatase classification"
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| − | Phosphatases | + | __NOTOC__ |
| + | Phosphatases are classified by protein structural fold of the catalytic domain, and sub-classified by families and subfamilies based on the sequence of the phosphatase domains as well as by sequences outside of the catalytic domain, and known biochemical and biological functions <cite>Chen</cite>. | ||
== Classification Chart of Protein Phosphatases == | == Classification Chart of Protein Phosphatases == | ||
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| bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_Paladin|Paladin]]|| bgcolor="#ffffff" colspan="1" | inactive || bgcolor="#ffffff" colspan="1" | Yes | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_Paladin|Paladin]]|| bgcolor="#ffffff" colspan="1" | inactive || bgcolor="#ffffff" colspan="1" | Yes | ||
|- | |- | ||
| − | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_OCA|OCA]]|| bgcolor="#ffffff" colspan="1" | ? || bgcolor="#ffffff" colspan="1" | | + | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_OCA|OCA]]|| bgcolor="#ffffff" colspan="1" | ? || bgcolor="#ffffff" colspan="1" | No |
|- | |- | ||
|bgcolor="#ffffff" rowspan="3" |[[Phosphatase_Fold_CC2|CC2]]||bgcolor="#ffffff" rowspan="3" |[[Phosphatase_Superfamily_CC2|CC2]] || bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_LMWPTP|LMWPTP]]|| bgcolor="#ffffff" colspan="1" | pTyr || bgcolor="#ffffff" colspan="1" | Yes | |bgcolor="#ffffff" rowspan="3" |[[Phosphatase_Fold_CC2|CC2]]||bgcolor="#ffffff" rowspan="3" |[[Phosphatase_Superfamily_CC2|CC2]] || bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_LMWPTP|LMWPTP]]|| bgcolor="#ffffff" colspan="1" | pTyr || bgcolor="#ffffff" colspan="1" | Yes | ||
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| bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_SSU72|SSU72]]|| bgcolor="#ffffff" colspan="1" | pSer || bgcolor="#ffffff" colspan="1" | Yes | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_SSU72|SSU72]]|| bgcolor="#ffffff" colspan="1" | pSer || bgcolor="#ffffff" colspan="1" | Yes | ||
|- | |- | ||
| − | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_ArsC|ArsC]]|| bgcolor="#ffffff" colspan="1" | Arsenate || bgcolor="#ffffff" colspan="1" | | + | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_ArsC|ArsC]]|| bgcolor="#ffffff" colspan="1" | Arsenate || bgcolor="#ffffff" colspan="1" | No |
|- | |- | ||
|bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Fold_Rhodanese|CC3]]||bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Superfamily_CC3|CC3]]|| bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_CDC25|CDC25]]|| bgcolor="#ffffff" colspan="1" | pTyr, pThr || bgcolor="#ffffff" colspan="1" | Yes | |bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Fold_Rhodanese|CC3]]||bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Superfamily_CC3|CC3]]|| bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_CDC25|CDC25]]|| bgcolor="#ffffff" colspan="1" | pTyr, pThr || bgcolor="#ffffff" colspan="1" | Yes | ||
|- | |- | ||
| − | |bgcolor="#ffffff" rowspan="3" |[[ | + | |bgcolor="#ffffff" rowspan="3" |[[Phosphatase_Fold_HAD|HAD]]||bgcolor="#ffffff" rowspan="3" |[[Phosphatase_Superfamily_HAD|HAD]]|| bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_EYA|EYA]]|| bgcolor="#ffffff" colspan="1" | pTyr || bgcolor="#ffffff" colspan="1" | Yes |
|- | |- | ||
|bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_FCP|FCP]]|| bgcolor="#ffffff" colspan="1" | pSer || bgcolor="#ffffff" colspan="1" | Yes | |bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_FCP|FCP]]|| bgcolor="#ffffff" colspan="1" | pSer || bgcolor="#ffffff" colspan="1" | Yes | ||
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|bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_NagD|NagD]]|| bgcolor="#ffffff" colspan="1" | pTyr, pSer || bgcolor="#ffffff" colspan="1" | Yes | |bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_NagD|NagD]]|| bgcolor="#ffffff" colspan="1" | pTyr, pSer || bgcolor="#ffffff" colspan="1" | Yes | ||
|- | |- | ||
| − | |bgcolor="#ffffff" rowspan="2" |[[ | + | |bgcolor="#ffffff" rowspan="2" |[[Phosphatase_Fold_PPPL|PPPL]]||bgcolor="#ffffff" rowspan="2" |[[Phosphatase_Superfamily_PPPL|PPPL]] || bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_PPP|PPP]]|| bgcolor="#ffffff" colspan="1" | pSer/pThr || bgcolor="#ffffff" colspan="1" | Yes |
|- | |- | ||
|bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_PAP|PAP]] || bgcolor="#ffffff" colspan="1" | ? || bgcolor="#ffffff" colspan="1" | Yes | |bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_PAP|PAP]] || bgcolor="#ffffff" colspan="1" | ? || bgcolor="#ffffff" colspan="1" | Yes | ||
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|} | |} | ||
| − | Synonymns: CC3 | + | Synonymns: CC3 = Rhodanese; PPM = PP2C. |
| − | Abbreviations: CC1, Cysteine-based Class I; CC2, Cysteine-based Class II; CC3, Cysteine-based Class III; | + | Abbreviations: CC1, Cysteine-based Class I; CC2, Cysteine-based Class II; CC3, Cysteine-based Class III; PPPL: PPP-like; PAP, Purple Acid Phosphatase; AP, Alkaline Phosphatase; HP, Histidine Phosphatase; HP1, Histidine Phosphatase, branch 1; HP2, Histidine Phosphatase, branch 2; CTD, RNA Poly II C-Terminal Domain. |
| − | == | + | === Notes of classification === |
| − | == [[Other_Classification_Schemes|Other Classification Schemes]] == | + | ===== [[CTD_Phosphorylation|Phosphorylation of RNA polymerase II C-terminal domain]] ===== |
| + | Both FCPs of HAD fold and SSU72 of CC2 fold can dephosphorylate CTD. | ||
| + | |||
| + | ===== [[PTPLA|PTPLA is a dubious phosphatase]] ===== | ||
| + | Notes on the PTPLA/PTP-like family that was claimed to be a phosphatase, but probably is not. | ||
| + | |||
| + | ===== [[Non-protein_phosphatases|Non-protein phosphatases]] ===== | ||
| + | Some phosphatases only dephosphorylate non-protein substrates, as far as known. | ||
| + | |||
| + | ===== [[Other_Classification_Schemes|Other Classification Schemes]] ===== | ||
| + | |||
| + | === Technical notes === | ||
| + | * What are the [[Single-Gene_Subfamilies_in_Nine_Genomes|single-gene subfamilies in nine genomes]]. We keep them because they are found in at least two genera, although they are not found in the other genome among the nine genomes: dicty, budding yeast, monosiga, sponge, nematostella, C. elegans, Drosophila, sea urchin, and human. | ||
| + | |||
| + | ===References=== | ||
| + | <biblio> | ||
| + | #Chen pmid=28400531 | ||
| + | </biblio> | ||
Latest revision as of 23:51, 13 April 2017
Phosphatases are classified by protein structural fold of the catalytic domain, and sub-classified by families and subfamilies based on the sequence of the phosphatase domains as well as by sequences outside of the catalytic domain, and known biochemical and biological functions [1].
Classification Chart of Protein Phosphatases
| Fold | Superfamily | Family | Substrate | Present in human |
|---|---|---|---|---|
| CC1 | CC1 | PTP | pTyr | Yes |
| DSP | pTyr, pSer/pThr, small molecule | Yes | ||
| PTEN | lipid | Yes | ||
| Myotubularin | lipid | Yes | ||
| SAC | lipid | Yes | ||
| Paladin | inactive | Yes | ||
| OCA | ? | No | ||
| CC2 | CC2 | LMWPTP | pTyr | Yes |
| SSU72 | pSer | Yes | ||
| ArsC | Arsenate | No | ||
| CC3 | CC3 | CDC25 | pTyr, pThr | Yes |
| HAD | HAD | EYA | pTyr | Yes |
| FCP | pSer | Yes | ||
| NagD | pTyr, pSer | Yes | ||
| PPPL | PPPL | PPP | pSer/pThr | Yes |
| PAP | ? | Yes | ||
| PPM | PPM | PPM | pSer/pThr | Yes |
| AP | AP | AP | pTyr, perhaps pSer/pThr | Yes |
| HP | HP | HP1 | pTyr, pSer/pThr | Yes |
| HP2 | pTyr, small molecules | Yes | ||
| PHP | PHP | PHP | pHis | Yes |
| RTR1 | RTR1 | RTR1 | pSer of CTD repeats | Yes |
Synonymns: CC3 = Rhodanese; PPM = PP2C.
Abbreviations: CC1, Cysteine-based Class I; CC2, Cysteine-based Class II; CC3, Cysteine-based Class III; PPPL: PPP-like; PAP, Purple Acid Phosphatase; AP, Alkaline Phosphatase; HP, Histidine Phosphatase; HP1, Histidine Phosphatase, branch 1; HP2, Histidine Phosphatase, branch 2; CTD, RNA Poly II C-Terminal Domain.
Notes of classification
Phosphorylation of RNA polymerase II C-terminal domain
Both FCPs of HAD fold and SSU72 of CC2 fold can dephosphorylate CTD.
PTPLA is a dubious phosphatase
Notes on the PTPLA/PTP-like family that was claimed to be a phosphatase, but probably is not.
Non-protein phosphatases
Some phosphatases only dephosphorylate non-protein substrates, as far as known.
Other Classification Schemes
Technical notes
- What are the single-gene subfamilies in nine genomes. We keep them because they are found in at least two genera, although they are not found in the other genome among the nine genomes: dicty, budding yeast, monosiga, sponge, nematostella, C. elegans, Drosophila, sea urchin, and human.
