Phosphatase Superfamily HP - Revision history

Gerard at 03:36, 9 May 2016

2016-05-09T03:36:45Z

Mark at 17:23, 2 June 2015

2015-06-02T17:23:38Z

Mark: /* Families */

2015-06-02T17:21:42Z

‎Families

Gerard at 20:50, 7 April 2015

2015-04-07T20:50:06Z

Gerard at 20:49, 7 April 2015

2015-04-07T20:49:07Z

Gerard at 05:41, 5 January 2015

2015-01-05T05:41:09Z

Mark: /* Classification */

2015-01-01T19:24:05Z

‎Classification

Mark: /* Classification */

2015-01-01T19:21:25Z

‎Classification

Mark at 19:21, 1 January 2015

2015-01-01T19:21:03Z

Mark at 19:18, 1 January 2015

2015-01-01T19:18:20Z

← Older revision		Revision as of 03:36, 9 May 2016
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		+	__NOTOC__
	[[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)

@@ Line 1: / Line 1: @@
 [[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_HP|Fold HP]]: [[Phosphatase_Superfamily_HP|Superfamily HP]] (histidine phosphatase)
-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>).
+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) =====

@@ Line 6: / Line 6: @@
 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>.
-===== Families  =====
+===== Classification schemes  =====
 The fold/superfamily HP  consists of two families based upon sequence similarity <cite>rigden08</cite>:
 * [[Phosphatase_Family_HP1|Branch 1]]
@@ Line 20: / Line 20: @@
 * Bisphosphoglycerate mutase (bPGM) - catalyzes primarily the interconversion of 1,3-phosphoglycerate (13PGA) and 23PGA
-====== Pfam ======
+====== 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.
-======  SCOP ======
+======  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:
 * c.60.1.1: Cofactor-dependent phosphoglycerate mutase

@@ Line 1: / Line 1: @@
 [[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_HP|Fold HP]]: [[Phosphatase_Superfamily_HP|Superfamily HP]] (histidine phosphatase)
-HP (histidine phosphatase, also known as phosphoglycerate mutase (PGM)) have a catalytic histidine which is phosphorylated during catalysis <cite>rigden08</cite>, but do no transphosphorylate on histidine. 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>).
+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>).
 ===== Naming: histidine phosphatase (HP) or phosphoglycerate mutase (PGM) =====

@@ Line 1: / Line 1: @@
 [[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_HP|Fold HP]]: [[Phosphatase_Superfamily_HP|Superfamily HP]] (histidine phosphatase)
-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>).
+HP (histidine phosphatase, also known as phosphoglycerate mutase (PGM)) have a catalytic histidine which is phosphorylated during catalysis <cite>rigden08</cite>, but do no transphosphorylate on histidine. 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>).
 ===== 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 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.
+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>.
 ===== Families  =====

@@ Line 36: / Line 36: @@
 #rigden01 pmid=11514674
 #rigden08 pmid=18092946
 #Rigden pmid=18092946
 </biblio>

@@ Line 8: / Line 8: @@
 ===== Classification =====
 The fold/superfamily HP  consists of two families based upon sequence similarity <cite>rigden08</cite>:
-* [[Phosphatase_Family_HP1|branch 1]]
+* [[Phosphatase_Family_HP1|Branch 1]]
-* [[Phosphatase_Family_HP2|branch 2]]
+* [[Phosphatase_Family_HP2|Branch 2]]
 This classification is largely the same with [[#Pfam|Pfam]] classification.

@@ Line 7: / Line 7: @@
 ===== Classification =====
-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.
+The fold/superfamily HP  consists of two families based upon sequence similarity <cite>rigden08</cite>:
 ====== Traditional classification ======

← Older revision		Revision as of 19:18, 1 January 2015
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−	[[Phosphatase classification\|Phosphatase Classification]]: [[~~Phosphatase_Fold_PGM~~\|Fold ~~PGM~~]]: [[Phosphatase_Superfamily_HP\|Superfamily HP]] (histidine phosphatase)	+	[[Phosphatase classification\|Phosphatase Classification]]: [[Phosphatase_Fold_HP\|Fold HP]]: [[Phosphatase_Superfamily_HP\|Superfamily HP]] (histidine phosphatase)

−	Histidine phosphatase does '''not''' dephosphorylate pHis. It is named for the catalytic histidine which is phosphorylated during catalysis <cite>~~Rigden~~</cite>. ~~In fact, the~~ superfamily is a large functionally diverse group of proteins. For a complete of functions characterized members in the superfamily~~, see~~ Table 1 and Table S1 in <cite>~~Rigden~~</cite>). The superfamily ~~contains~~ two ~~branches sharing very limited~~ sequence similarity. ~~The superfamily~~ is ~~corresponding to His_phosphatase~~ in ~~PFAM database~~, Pfam ID [http://pfam.xfam.org/clan/~~cl0071~~ CL0071]).	+	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>).
		+
		+	===== 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 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: [[Phosphatase_Family_HP1\|branch 1]] and [[Phosphatase_Family_HP2\|branch 2]] <cite>rigden08</cite>. This classification is largely the same with [[#Pfam\|Pfam]] classification.
		+
		+	====== 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)
		+	** 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 [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.
		+
		+	====== SCOP ======
		+	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.60.1.2: 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 ===
		+	<biblio>
		+	#jedrzejas00 pmid=10958932
		+	#rigden01 pmid=11514674
		+	#rigden08 pmid=18092946
		+	</biblio>