Difference between revisions of "Phosphatase Superfamily HP"

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[[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_HP|Fold HP]]: [[Phosphatase_Superfamily_HP|Superfamily HP]] (histidine phosphatase)
 
[[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_HP|Fold HP]]: [[Phosphatase_Superfamily_HP|Superfamily HP]] (histidine phosphatase)
  
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HP is short for histidine phosphatase, which is also known as phosphoglycerate mutase (PGM). Histidine phosphatase does '''not''' dephosphorylate pHis. It  is named for the catalytic histidine which is phosphorylated during catalysis <cite>rigden08</cite>. The superfamily is a large functionally diverse group of proteins. For a complete of functions characterized members in the superfamily (Table 1 and Table S1 in <cite>rigen08</cite>).  
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HP (histidine phosphatase, also known as phosphoglycerate mutase (PGM)) phosphatases have a catalytic histidine which is phosphorylated during catalysis <cite>rigden08</cite>, but they do not dephosphorylate histidine on other proteins. The superfamily is a large functionally diverse group of proteins. For a complete of functions characterized members in the superfamily (Table 1 and Table S1 in <cite>rigen08</cite>). HPs are found in both prokaryotes and eukaryotes.
  
 
===== Naming: histidine phosphatase (HP) or phosphoglycerate mutase (PGM) =====
 
===== Naming: histidine phosphatase (HP) or phosphoglycerate mutase (PGM) =====
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The earliest and arguably best studied members of this group of genes primarily function as mutase, which results in naming them PGM. However, most if not all of later discoveries have been phosphatase activities of one kind or another <cite>rigden08</cite>. To reflect this fact, we call it histidine phosphatase rather than phosphoglycerate mutase, although the genes are sometimes referred as PGM in literature and SCOP database.
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The earliest and arguably best studied members of this group of genes primarily function as mutase, which results in naming them PGM. However, most if not all of later discoveries have been phosphatase activities <cite>rigden08</cite>.
  
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===== Classification =====
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===== Classification schemes  =====
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The fold/superfamily HP  consists of two families based upon sequence similarity: [[Phosphatase_Family_HP1|branch 1]] and [[Phosphatase_Family_HP2|branch 2]] <cite>rigden08</cite>. This classification is largely the same with [[#Pfam|Pfam]] classification.
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The fold/superfamily HP  consists of two families based upon sequence similarity <cite>rigden08</cite>:  
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* [[Phosphatase_Family_HP1|Branch 1]]  
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* [[Phosphatase_Family_HP2|Branch 2]]  
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This classification is largely the same with [[#Pfam|Pfam]] classification.
  
 
====== Traditional classification ======
 
====== Traditional classification ======
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* Bisphosphoglycerate mutase (bPGM) - catalyzes primarily the interconversion of 1,3-phosphoglycerate (13PGA) and 23PGA
 
* Bisphosphoglycerate mutase (bPGM) - catalyzes primarily the interconversion of 1,3-phosphoglycerate (13PGA) and 23PGA
  
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====== Pfam ======
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====== Pfam families ======
 
HP corresponds to [http://pfam.xfam.org/clan/CL0071 histidine phosphatase superfamily] in  [[Phosphatase_Glossary#Pfam|Pfam database]]. It contains two families: [http://pfam.xfam.org/family/PF00300 branch 1] and [http://pfam.xfam.org/family/PF00328 branch 2]. Branch 1 includes dPGMs, branch 2 includes histidine acid phosphatase. Branch 1 is largely dPGM.
 
HP corresponds to [http://pfam.xfam.org/clan/CL0071 histidine phosphatase superfamily] in  [[Phosphatase_Glossary#Pfam|Pfam database]]. It contains two families: [http://pfam.xfam.org/family/PF00300 branch 1] and [http://pfam.xfam.org/family/PF00328 branch 2]. Branch 1 includes dPGMs, branch 2 includes histidine acid phosphatase. Branch 1 is largely dPGM.
  
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======  SCOP ======
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======  SCOP classification ======
 
HP corresponds to [[Phosphatase_Glossary#SCOP|SCOP]] fold [http://scop.berkeley.edu/sunid=53253 phosphoglycerate mutase-like (c.60)]. It contains single superfamily, which include the families below:
 
HP corresponds to [[Phosphatase_Glossary#SCOP|SCOP]] fold [http://scop.berkeley.edu/sunid=53253 phosphoglycerate mutase-like (c.60)]. It contains single superfamily, which include the families below:
 
* c.60.1.1: Cofactor-dependent phosphoglycerate mutase
 
* c.60.1.1: Cofactor-dependent phosphoglycerate mutase
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#rigden01 pmid=11514674
 
#rigden01 pmid=11514674
 
#rigden08 pmid=18092946
 
#rigden08 pmid=18092946
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</biblio>
 
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<biblio>
 
 
#Rigden pmid=18092946
 
#Rigden pmid=18092946
 
</biblio>
 
</biblio>

Latest revision as of 03:36, 9 May 2016

Phosphatase Classification: Fold HP: Superfamily HP (histidine phosphatase)

HP (histidine phosphatase, also known as phosphoglycerate mutase (PGM)) phosphatases have a catalytic histidine which is phosphorylated during catalysis [1], but they do not dephosphorylate histidine on other proteins. The superfamily is a large functionally diverse group of proteins. For a complete of functions characterized members in the superfamily (Table 1 and Table S1 in [2]). HPs are found in both prokaryotes and eukaryotes.

Naming: histidine phosphatase (HP) or phosphoglycerate mutase (PGM)

The earliest and arguably best studied members of this group of genes primarily function as mutase, which results in naming them PGM. However, most if not all of later discoveries have been phosphatase activities [1].

Classification schemes

The fold/superfamily HP consists of two families based upon sequence similarity [1]:

This classification is largely the same with Pfam classification.

Traditional classification

Traditionally, HP/PGM is classified as below [3, 4]:

  • Monophosphoglycerate mutase (mPGM) - catalyzes the interconversion of 3-phosphoglycerate (3PGA) and 2-phosphoglycerate (2PGA)
    • dependent on 23PGA as a cofactor (dPGM) - found in animal, fungi, and bacteria
    • independent of 23PGA as a cofactor (iPGM) - found in plants, and bacteria
  • Bisphosphoglycerate mutase (bPGM) - catalyzes primarily the interconversion of 1,3-phosphoglycerate (13PGA) and 23PGA
Pfam families

HP corresponds to histidine phosphatase superfamily in Pfam database. It contains two families: branch 1 and branch 2. Branch 1 includes dPGMs, branch 2 includes histidine acid phosphatase. Branch 1 is largely dPGM.

SCOP classification

HP corresponds to SCOP fold phosphoglycerate mutase-like (c.60). It contains single superfamily, which include the families below:

  • c.60.1.1: Cofactor-dependent phosphoglycerate mutase
  • c.60.1.2: Histidine acid phosphatase
  • c.60.1.4: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain

c60.1.1 and c60.1.4 forms dPGM.

References

  1. Rigden DJ. The histidine phosphatase superfamily: structure and function. Biochem J. 2008 Jan 15;409(2):333-48. DOI:10.1042/BJ20071097 | PubMed ID:18092946 | HubMed [rigden08]
  2. Jedrzejas MJ. Structure, function, and evolution of phosphoglycerate mutases: comparison with fructose-2,6-bisphosphatase, acid phosphatase, and alkaline phosphatase. Prog Biophys Mol Biol. 2000;73(2-4):263-87. DOI:10.1016/s0079-6107(00)00007-9 | PubMed ID:10958932 | HubMed [jedrzejas00]
  3. Rigden DJ, Bagyan I, Lamani E, Setlow P, and Jedrzejas MJ. A cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus is actually a broad specificity phosphatase. Protein Sci. 2001 Sep;10(9):1835-46. DOI:10.1110/ps.15701 | PubMed ID:11514674 | HubMed [rigden01]
  4. Rigden DJ. The histidine phosphatase superfamily: structure and function. Biochem J. 2008 Jan 15;409(2):333-48. DOI:10.1042/BJ20071097 | PubMed ID:18092946 | HubMed [Rigden]
All Medline abstracts: PubMed | HubMed
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