Difference between revisions of "Phosphatase Fold HP"
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m (Mark moved page Phosphatase Fold PGM to Phosphatase Fold HP) |
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| − | [[Phosphatase classification|Phosphatase Classification]]: [[ | + | [[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_HP|Fold HP]] |
| − | + | HP is short for histidine phosphatase, which is also known as phosphoglycerate mutase (PGM). | |
| + | ===== Naming: histidine phosphatase and phosphoglycerate mutase ===== | ||
| + | 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. | ||
| + | |||
| + | ===== Classification ===== | ||
| + | The fold/superfamily HP consists of two families based upon sequence similarity: branch 1 and branch 2 <cite>rigden08</cite>. This classification is largely the same with [[#Pfam|Pfam]] database. | ||
| + | |||
| + | ====== Traditional classification ====== | ||
| + | Traditionally, HP/PGM is classified as below <cite>jedrzejas00, rigden01</cite>: | ||
* Monophosphoglycerate mutase (mPGM) - catalyzes the interconversion of 3-phosphoglycerate (3PGA) and 2-phosphoglycerate (2PGA) | * 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 | ** dependent on 23PGA as a cofactor (dPGM) - found in animal, fungi, and bacteria | ||
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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 | ||
| − | ===== | + | ====== Pfam ====== |
| − | + | 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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===== [[Phosphatase_Glossary#SCOP|SCOP]] ===== | ===== [[Phosphatase_Glossary#SCOP|SCOP]] ===== | ||
| − | + | HP corresponds to 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 | ||
* c.60.1.2: Histidine acid phosphatase | * c.60.1.2: Histidine acid phosphatase | ||
Revision as of 19:11, 1 January 2015
Phosphatase Classification: Fold HP
HP is short for histidine phosphatase, which is also known as phosphoglycerate mutase (PGM).
Contents
Naming: histidine phosphatase and phosphoglycerate mutase
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 [1]. 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.
Classification
The fold/superfamily HP consists of two families based upon sequence similarity: branch 1 and branch 2 [1]. This classification is largely the same with Pfam database.
Traditional classification
Traditionally, HP/PGM is classified as below [2, 3]:
- 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
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
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
- 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 |
- 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 |
