Difference between revisions of "Main Page"

From PhosphataseWiki
Jump to: navigation, search
(Phosphatase Classification)
 
(70 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
Welcome to Phosphatase Wikepedia, a resource for of phosphatases and phosphatase signaling. This is a pilot project for sharing and publication of discoveries that do not fit into traditional publications or haven't yet been polished for publication. Initial content is mostly from the Manning lab at Salk, but we welcome anyone who would like to contribute. Like other wiki's, just go to the login page to request an account.
+
Welcome to Phosphatase Wiki, a resource for phosphatases and phosphatase signaling focused on genomics and evolution. This is a pilot project for sharing and publication of discoveries that do not fit into traditional publications or haven't yet been polished for publication. This also includes supporting data and results for our 2017 Science Signaling paper on the genomics and evolution of phosphatases <cite>Chen</cite>.  Initial content is mostly from the Manning lab at Salk (moved to Genentech in 2012), but we welcome anyone who would like to contribute. Like other wikis, just go to the login page to request an account.
  
 +
== [[phosphatase classification|Protein Phosphatase Classification and Evolution]] ==
 +
This is the heart of this wiki - a set of articles on individual families, subfamilies and folds of phosphatases, with a focus on genomics, evolution, and biological functions shared across organisms.
  
===[[Introduction to Phosphatases]]===
+
===== [[Phosphatase_classification#Classification_Chart_of_Protein_Phosphatases|Classification chart]] =====
 +
In contrast with kinases, there are multiple folds of protein phosphatases, which means protein phosphatases have multiple independent evolutionary origins, while most kinases have a single origin. We classified protein phosphatases into a hierarchy scheme of four levels: fold, superfamily, family and subfamily.
  
=== [[phosphatase classification|Phosphatase Classification]]===
+
===== [[Pseudophosphatases]] =====
Of the hundreds of phosphatases in the genome, how are they organized and classified?
+
Some phosphatases are catalytically inactive, due to alterations in the active site, but are conserved and frequently function in signaling pathways.
  
Pending (the hybrid scheme of classification; alternative schemes: PTP and Ser/Thr phosphatase by substrate).
+
===== Protein phosphatase evolution =====
 +
Each of the protein phosphatase fold are able to be found in early eukaryotes, so are most of the protein phosphatase families. The subfamilies have a dynamic evolutionary pattern. Some subfamilies have been lost multiple times through independent evolutionary events. While many subfamilies expanded in gene number in vertebrates, some subfamily has a single member in almost all the sequenced eukaryotic genomes. Protein phosphatase also underwent [[Accesory_Domain_Gains_and_Losses|gains and losses of accessory domain]].
  
== Classification Chart ==
+
===== [[Human_Protein_Phosphatase_Pseudogene|Human protein phosphatase pseudogenes]] =====
 +
There are about 80 pseudogenes which originated from the protein-coding genes that encode protein phosphatases in human. They are functional at least in some cases. For instance, PTENP1 is a processed pseudogene of PTEN and regulates PTEN by both sense and antisense RNAs.
  
{| 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" align="center" |Group|| bgcolor="#ffffff" colspan="1" align="center" |Family|| bgcolor="#ffffff" colspan="1" align="center"| Substrate
 
|-
 
|bgcolor="#ffffff" rowspan="4" align="center" |Cys-based Group I|| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_HMWPTP|Classic PTP]]|| bgcolor="#ffffff" colspan="1" align="center"| pTyr
 
|-
 
| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_DSP_PTEN|DSP and PTEN]]|| bgcolor="#ffffff" colspan="1" align="center"| pTyr, pSer/pThr, lipid
 
|-
 
| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_Myotubularin|Myotubularin]]|| bgcolor="#ffffff" colspan="1" align="center"| lipid
 
|-
 
| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_OCA|OCA]]|| bgcolor="#ffffff" colspan="1" align="center"| ?
 
|-
 
|bgcolor="#ffffff" rowspan="1" align="center" |Cys-based Group II|| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_CDC25|CDC25]]|| bgcolor="#ffffff" colspan="1" align="center"| pTyr, pThr
 
|-
 
|bgcolor="#ffffff" rowspan="2" align="center" |Cys-based Group III|| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_LMWPTP|LMWPTP]]|| bgcolor="#ffffff" colspan="1" align="center"| pTyr
 
|-
 
| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_SSU72|SSU72]]|| bgcolor="#ffffff" colspan="1" align="center"| pSer
 
|-
 
|bgcolor="#ffffff" rowspan="4" align="center" |[[Phosphatase_Group_HAD|HAD]]|| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_EYA|EYA]]|| bgcolor="#ffffff" colspan="1" align="center"| pTyr
 
|-
 
|bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_FCP|FCP]]|| bgcolor="#ffffff" colspan="1" align="center"| pSer
 
|-
 
|bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_NagD|NagD]]|| bgcolor="#ffffff" colspan="1" align="center"| pTyr, pSer
 
|-
 
|bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_MDP1|MDP1]]|| bgcolor="#ffffff" colspan="1" align="center"| pTyr?
 
|-
 
|bgcolor="#ffffff" rowspan="1" align="center" |PPP|| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_PPP|PPP]]|| bgcolor="#ffffff" colspan="1" align="center"| pSer/pThr
 
|-
 
|bgcolor="#ffffff" rowspan="1" align="center" |PPM (PP2C)|| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_PPM|PPM (PP2C)]]|| bgcolor="#ffffff" colspan="1" align="center"| pSer/pThr
 
|-
 
|bgcolor="#ffffff" rowspan="1" align="center" |PHP|| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_PHP|PHP]]|| bgcolor="#ffffff" colspan="1" align="center"| pHis
 
|-
 
|bgcolor="#ffffff" rowspan="1" align="center" |PHP|| bgcolor="#ffffff" colspan="1" align="center" |[[Phosphatase_Family_Rtr1|RTR1]]|| bgcolor="#ffffff" colspan="1" align="center"| pSer
 
|}
 
  
== [[Other_Classification_Schemes|Other Classification Schemes]] ==
+
==Additional Topics==
  
== [[other_phosphatase|Other phosphatases]] ==
 
  
===[[Protein Phosphatase Evolution]]===
+
* [[Phosphatases_and_Diseases|Phosphatases and diseases]]  
Where did they all come from, and how did they get to where they are today?
+
* [[Drug_Targeting_Phosphatases|Phosphatases as drug and/or inhibitor targets]]
 +
* [[Dephosphorylation_on_unusual_amino_acids|(De)phosphorylation on unusual amino acids]]: unusual evidence for phosphorylation on histidine, aspartate, cysteine, lysine, and arginine.
 +
* [[Introduction to Phosphatases]]
  
==Topics==
+
== [[Phosphatase_Glossary|Phosphatase Glossary]] ==
===[[CTD_Phosphorylation|Phosphorylation of RNA polymerase II C-terminal domain]]===
+
The C-terminal domain of RNA polymerase II's largest subunit undergoes dynamic phosphorylation during transcription, and the different phosphorylation patterns that predominate at each stage of transcription recruit the appropriate set of mRNA-processing and histone-modifying factors. This complex phosphorylation patterns are regulated by quite a few phosphatases and kinases.
+
  
===[[Network|Phosphatase-Substrate-Kinase Network]]===
+
== [[Technical_Notes|Technical Notes]] ==
The network is based upon biological knowledge. Six types of relationship between phosphatases and kinases are recorded: 1) they work on the same substrate, 2) phosphatase dephosphorylates kinase, 3) kinase phosphorylates phosphatase, 4) binding but no reported (de)phosphorylated interaction, 5) functional relationship, but not direct interaction, and 6) no relationship.
+
  
===[[Dephosphorylation on unusual amino acids]]===
+
==[[Sandbox]]==
Unusual evidence for phosphorylation on histidine, aspartate, cysteine, lysine, and arginine.
+
 
 +
 
 +
===References===
 +
<biblio>
 +
#Chen pmid=28400531
 +
</biblio>

Latest revision as of 16:04, 13 April 2017

Welcome to Phosphatase Wiki, a resource for phosphatases and phosphatase signaling focused on genomics and evolution. This is a pilot project for sharing and publication of discoveries that do not fit into traditional publications or haven't yet been polished for publication. This also includes supporting data and results for our 2017 Science Signaling paper on the genomics and evolution of phosphatases [1]. Initial content is mostly from the Manning lab at Salk (moved to Genentech in 2012), but we welcome anyone who would like to contribute. Like other wikis, just go to the login page to request an account.

Protein Phosphatase Classification and Evolution

This is the heart of this wiki - a set of articles on individual families, subfamilies and folds of phosphatases, with a focus on genomics, evolution, and biological functions shared across organisms.

Classification chart

In contrast with kinases, there are multiple folds of protein phosphatases, which means protein phosphatases have multiple independent evolutionary origins, while most kinases have a single origin. We classified protein phosphatases into a hierarchy scheme of four levels: fold, superfamily, family and subfamily.

Pseudophosphatases

Some phosphatases are catalytically inactive, due to alterations in the active site, but are conserved and frequently function in signaling pathways.

Protein phosphatase evolution

Each of the protein phosphatase fold are able to be found in early eukaryotes, so are most of the protein phosphatase families. The subfamilies have a dynamic evolutionary pattern. Some subfamilies have been lost multiple times through independent evolutionary events. While many subfamilies expanded in gene number in vertebrates, some subfamily has a single member in almost all the sequenced eukaryotic genomes. Protein phosphatase also underwent gains and losses of accessory domain.

Human protein phosphatase pseudogenes

There are about 80 pseudogenes which originated from the protein-coding genes that encode protein phosphatases in human. They are functional at least in some cases. For instance, PTENP1 is a processed pseudogene of PTEN and regulates PTEN by both sense and antisense RNAs.


Additional Topics

Phosphatase Glossary

Technical Notes

Sandbox

References

  1. Chen MJ, Dixon JE, and Manning G. Genomics and evolution of protein phosphatases. Sci Signal. 2017 Apr 11;10(474). DOI:10.1126/scisignal.aag1796 | PubMed ID:28400531 | HubMed [Chen]