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 == | + | == Classification Chart of Protein Phosphatases == |
{| class="wikitable" border="2" style="background: #ffffff; border: 1px #000000 solid; border-collapse: collapse; font-size: 100%;" cellpadding="5" cellspacing="10" | {| class="wikitable" border="2" style="background: #ffffff; border: 1px #000000 solid; border-collapse: collapse; font-size: 100%;" cellpadding="5" cellspacing="10" | ||
|- | |- | ||
− | !bgcolor="#ffffff" rowspan="1" | + | !bgcolor="#ffffff" rowspan="1" |Fold||bgcolor="#ffffff" rowspan="1" |Superfamily|| bgcolor="#ffffff" colspan="1" |Family|| bgcolor="#ffffff" colspan="1" | Substrate|| bgcolor="#ffffff" colspan="1" | Present in human |
|- | |- | ||
− | |bgcolor="#ffffff" rowspan=" | + | |bgcolor="#ffffff" rowspan="7" | [[Phosphatase_Fold_CC1|CC1]]||bgcolor="#ffffff" rowspan="7" | [[Phosphatase_Superfamily_CC1|CC1]] || bgcolor="#ffffff" colspan="1" | [[Phosphatase_Family_PTP|PTP]]|| bgcolor="#ffffff" colspan="1" | pTyr || bgcolor="#ffffff" colspan="1" | Yes |
|- | |- | ||
− | | bgcolor="#ffffff" colspan="1" | + | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_DSP|DSP]]|| bgcolor="#ffffff" colspan="1" | pTyr, pSer/pThr, small molecule || bgcolor="#ffffff" colspan="1" | Yes |
|- | |- | ||
− | | bgcolor="#ffffff" colspan="1" | + | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_PTEN|PTEN]]|| bgcolor="#ffffff" colspan="1" | lipid || bgcolor="#ffffff" colspan="1" | Yes |
|- | |- | ||
− | | bgcolor="#ffffff" colspan="1" | + | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_Myotubularin|Myotubularin]]|| bgcolor="#ffffff" colspan="1" | lipid || bgcolor="#ffffff" colspan="1" | Yes |
|- | |- | ||
− | + | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_Sac|SAC]]|| bgcolor="#ffffff" colspan="1" | lipid || 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" | + | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_OCA|OCA]]|| bgcolor="#ffffff" colspan="1" | ? || bgcolor="#ffffff" colspan="1" | No |
|- | |- | ||
− | | bgcolor="#ffffff" | + | |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" colspan="1" |[[Phosphatase_Family_SSU72|SSU72]]|| bgcolor="#ffffff" colspan="1" | pSer || bgcolor="#ffffff" colspan="1" | Yes | |
|- | |- | ||
− | |bgcolor="#ffffff" colspan="1" | + | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_ArsC|ArsC]]|| bgcolor="#ffffff" colspan="1" | Arsenate || bgcolor="#ffffff" colspan="1" | No |
|- | |- | ||
− | |bgcolor="#ffffff" | + | |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" | + | |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_NagD|NagD]]|| bgcolor="#ffffff" colspan="1" | pTyr, pSer || bgcolor="#ffffff" colspan="1" | Yes | |
|- | |- | ||
− | |bgcolor="#ffffff" rowspan=" | + | |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" rowspan="1" | + | |bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_PAP|PAP]] || bgcolor="#ffffff" colspan="1" | ? || bgcolor="#ffffff" colspan="1" | Yes |
+ | |- | ||
+ | |bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Fold_PPM|PPM]]||bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Superfamily_PPM|PPM]]|| bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_PPM|PPM]]|| bgcolor="#ffffff" colspan="1" | pSer/pThr || bgcolor="#ffffff" colspan="1" | Yes | ||
+ | |- | ||
+ | |bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Fold_AP|AP]]||bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Superfamily_AP|AP]] || bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_AP|AP]]|| bgcolor="#ffffff" colspan="1" | pTyr, perhaps pSer/pThr || bgcolor="#ffffff" colspan="1" | Yes | ||
+ | |- | ||
+ | |bgcolor="#ffffff" rowspan="2" |[[Phosphatase_Fold_HP|HP]]||bgcolor="#ffffff" rowspan="2" |[[Phosphatase_Superfamily_HP|HP]] || bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_HP1|HP1]]|| bgcolor="#ffffff" colspan="1" | pTyr, pSer/pThr || bgcolor="#ffffff" colspan="1" | Yes | ||
+ | |- | ||
+ | | bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_HP2|HP2]]|| bgcolor="#ffffff" colspan="1" | pTyr, small molecules || bgcolor="#ffffff" colspan="1" | Yes | ||
+ | |- | ||
+ | |bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Fold_PHP|PHP]]||bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Superfamily_PHP|PHP]]|| bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_PHP|PHP]]|| bgcolor="#ffffff" colspan="1" | pHis || bgcolor="#ffffff" colspan="1" | Yes | ||
+ | |- | ||
+ | |bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Fold_RTR1|RTR1]]||bgcolor="#ffffff" rowspan="1" |[[Phosphatase_Superfamily_RTR1|RTR1]]|| bgcolor="#ffffff" colspan="1" |[[Phosphatase_Family_RTR1|RTR1]]|| bgcolor="#ffffff" colspan="1" | pSer of CTD repeats || bgcolor="#ffffff" colspan="1" | 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 === | ||
+ | |||
+ | ===== [[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.