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Kinase Family GAPDH

2012-05-10T14:34:54Z

← Older revision		Revision as of 14:34, 10 May 2012
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	The glycolytic enzyme, Glyceraldehyde-3-phosphate dehydrogenase has been demonstrated to have a kinase activity towards viral proteins, a GABA receptor, and in vitro.		The glycolytic enzyme, Glyceraldehyde-3-phosphate dehydrogenase has been demonstrated to have a kinase activity towards viral proteins, a GABA receptor, and in vitro.
		+
		+	====GAPDH and Glycolysis====
		+	GAPDH has a kinase function during glycolysis: it first oxidizes glyceraldehyde 3-phosphate, converting the aldehyde group to a carboxylic acid, and then adds inorganic phosphate to the alcohol group of that carboxylic acid ([http://en.wikipedia.org/wiki/Glyceraldehyde_3-phosphate_dehydrogenase Wikipedia]). GAPDH uses the energy from the first reaction to drive the unusual, and energetically unfavorable, phosphorylation with orthophosphate (Pi). The next step in glycolysis inovlves phosphoglycerate kinase (PGK) acting as a form of phosphatase or reverse kinase: it removes one of the phosphates on the glyceraldehyde diphosphate by converting ADP to ATP.

	====Evidence for Protein Kinase Activity====		====Evidence for Protein Kinase Activity====
-	GAPDH from rabbit muscle was reported to ~~autophorphorylate~~ and transphosphorylate two uncharacterized proteins <cite>Kawamoto</cite>. Transphosphorylation appeared to involve transfer of the phosphate originally used to autophosphorylate, using ATP as a donor. The pH lability profile of the autophosphorylated form suggested the presence of an acyl phosphate (probably phosphorylation of carboxylic acid) rather than the typical ester phosphates of Ser/Thr/Tyr phosphorylation.	+	GAPDH from rabbit muscle was reported to autophosphorylate and transphosphorylate two uncharacterized proteins <cite>Kawamoto</cite>. Transphosphorylation appeared to involve transfer of the phosphate originally used to autophosphorylate, using ATP as a donor. The pH lability profile of the autophosphorylated form suggested the presence of an acyl phosphate (probably phosphorylation of carboxylic acid) rather than the typical ester phosphates of Ser/Thr/Tyr phosphorylation.
-		+
-	GAPDH has a kinase function during glycolysis: it first oxidizes glyceraldehyde 3-phosphate, converting the aldehyde group to a carboxylic acid, and then adds inorganic phosphate to the alcohol group of that carboxylic acid ([http://en.wikipedia.org/wiki/Glyceraldehyde_3-phosphate_dehydrogenase Wikipedia]). GAPDH uses the energy from the first reaction to drive the unusual, and energetically unfavorable, phosphorylation with inorganic phosphate. The next step in glycolysis inovlves phosphoglycerate kinase acting as a form of phosphatase or reverse kinase: it removes one of the phosphates on the glyceraldehyde diphosphate by converting ADP to ATP.	+
-		+
-	~~HBV: <cite>Duclos-Vallee</cite>~~	+
-	~~GABAa: <cite>Laschet</cite>~~	+

		+	GAPDH has been reported to phosphorylate GABRA1, a subunit of the receptor for the inhibitory neurotransmitter GABA <cite>Laschet</cite>. GAPDH binds tightly to GABRA1, and phosphorylates it on T337 and S416, both residues found within a conserved Nxxx[S/T]K motif. Labeling experiments suggest that GAPDH and PGK produce ATP while anchored at the receptor, and that GAPDH uses this ATP to autophosphorylate and transphosphorylate the receptor. This system may have evolved from one where glycolytic enzymes are localized to the membrane to produce ATP to power ATPase-driven ion channels <cite>Silver, Wu</cite>, and suggests that the phosphorylation may be regulatory and may respond to levels of ATP/ADP/Pi, Mg++ or glycolytic precursors. A separate study <cite>Wu</cite> also reports GAPDH autophosphorylation at the neuronal post-synaptic density, and that autophosphorylated GAPDH had an increased affinity for binding actin.

-	~~A second role for mammalian~~ GAPDH in phos- phate group transfer was recently described by Engel et al. [39]. Their studies examined the structure and function of a gene family, termed nm23, which ex- hibited potential metastasis suppressor activity. However, the function of the gene product responsi- ble for this activity was unknown. Although it had been ~~established that~~ the nm23 tumor suppresser gene encoded a nucleoside diphosphate kinase activ- ity, it did not appear that such an activity was re- sponsible for its tumor suppressor action. An alter- native function was described for the nm23 protein ~~as a serine/threonine speci¢c phosphotransferase. Cu~~- riously, the highly puri¢ed nm23 protein did not ex- hibit this activity. Subsequently, in human cells, it was determined that it existed in a protein complex with a 37 kDa protein. The latter was identi¢ed as GAPDH by sequence analysis. Stoichiometric exami- nation suggested a 1:1 ratio and a molecular mass of 107.4 kDa, indicating a GAPDH dimer/nm23 dimer interaction. Of note, GAPDH glycolytic activity and diphosphate kinase activity were not inhibited by formation of this complex. Further, no reduction of phosphotransferase activity was observed in the pres- ence of 80 M NADH.	+	GAPDH has also been reported to phosphorylate the core protein of hepatitis B virus <cite>Duclos-Vallee</cite>.

		+	====Other Functions====
		+	GAPDH has also been reported to activate transcription, as part of the OCA-S complex, along with lactate dehydrogenase <cite>Zheng</cite>; may link NO signaling to apoptosis <cite>Hara</cite>; and be involved in ER-to-Golgi transport <cite>Tisdale</cite>

-	~~GADPH~~ is also the substrate or binding partner of typical protein kinases, including PKC, CAMK2 and EGFR, Src~~...~~	+	GAPDH is also the substrate or binding partner of typical protein kinases, including PKC, CAMK2 and EGFR, Src, and has been reported to be tightly bound to nucleoside diphosphate kinases (NDK)

	====Domain Structure====		====Domain Structure====
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	====References====		====References====
	<biblio>		<biblio>
		+	#Hara pmid=16505364
	#Kawamoto pmid=3955021		#Kawamoto pmid=3955021
	#Laschet pmid=15342727		#Laschet pmid=15342727
		+	#Tisdale pmid=17488287
		+	#Wu pmid=9371836
		+	#Zheng pmid=12887926
	</biblio>		</biblio>

	====Unlinked References====		====Unlinked References====
	#Duclos-Vallee pmid=9680129		#Duclos-Vallee pmid=9680129
		+	#Silver pmid=9145812

Kinase Family BRD

2012-05-10T13:11:07Z

← Older revision		Revision as of 13:11, 10 May 2012
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	====Evolution====		====Evolution====
-	Mammals have four BRDs (BRD2/RING3, BRD3, BRD4 and BRDT), Drosophila has one (fs(1)h) and C. elegans has 3. A more distantly related homolog is found in fungi (S. cerevisiae Bdf1 and homologs) ~~but~~ that ~~may~~ not ~~be truly~~ orthologous~~, as others have reported that~~ to ~~be a homolog of Taf1. Other~~ BRD ~~proteins are found across many eukaryotes~~.	+	Mammals have four BRDs (BRD2/RING3, BRD3, BRD4 and BRDT), Drosophila has one (fs(1)h) and C. elegans has 3. A more distantly related homolog is found in fungi (S. cerevisiae Bdf1 and homologs) and in plants. Other basal lineages have proteins with single bromodomains that are not clearly orthologous to BRD, but may have related functions.

	====Evidence for Protein Kinase Activity====		====Evidence for Protein Kinase Activity====
-	Human BRD2 was first identified as an autophosphorylating nuclear-specific protein in Hela extracts <cite>Denis</cite>. Recombinant BRD2 expressed in ''E. coli'' showed in vitro kinase activity. However, the kinase activity was only seen when the purified recombinant protein was first incubated with Hela cell extract and repurified. It was suggested that this incubation could allow BRD2 to be activated by phosphorylation, but it is also possible that this step allowed BRD2 to bind to a human kinase which was then responsible for the observed activity. Recombinant BRD2 purified from COS cells also showed in vitro kinase activity, without pre-incubation.	+	Human BRD2 was first identified as an autophosphorylating nuclear-specific protein in Hela extracts <cite>Denis</cite>. Recombinant BRD2 expressed in ''E. coli'' showed in vitro kinase activity. However, the kinase activity was only seen when the purified recombinant protein was first incubated with Hela cell extract and repurified. It was suggested that this incubation could allow BRD2 to be activated by phosphorylation, but it is also possible that this step allowed BRD2 to bind to a human kinase which was then responsible for the observed activity. Recombinant BRD2 purified from COS cells also showed in vitro kinase activity, without pre-incubation. Mutation of a C-terminal lysine (K578A) abolished the activity seen in ''E. coli'', implicating it either in cryptic kinase activity or binding to an active human kinase.

-	If the BRD kinase activity is due to a tightly bound kinase, the most likely candidate is CDK9. It is not known if BRD2 binds CDK9, but BRD4, BRDT and the Drosophila homolog, fs(1)h are all reported to bind CDK9, and BRD4 may induce CDK9 phosphorylation <cite>Zhou, Bisgrove</cite>.	+	If the BRD kinase activity is due to a tightly bound kinase, the most likely candidate is CDK9. It is not known if BRD2 binds CDK9, but BRD4, BRDT and the Drosophila homolog, fs(1)h are all reported to bind CDK9, and BRD4 may induce CDK9 phosphorylation <cite>Zhou, Bisgrove</cite>. Bdf1, the yeast BRD is also known to bind to CK2 kinase <cite>Sawa</cite>.

-	~~BRD contain two bromodomains and~~ a ~~novel conserved C~~-terminal ~~region~~, ~~as well as less~~-~~conserved regions~~. ~~None show an obvious similarity to any known kinases. Mutation~~ of a ~~C-terminal lysine (K578A) abolished the~~ activity seen in ''E. coli'', ~~implicating it either~~ in ~~cryptic~~ kinase ~~activity or binding~~ to ~~an active human kinase~~.	+	Human BRD4 has also been shown to be a kinase with autophosphorylation and transphosphorylation activity <cite>Devaiah</cite>. Deletion mutations mapped the kinase activity to the N-terminal half, from AA 1-699. Deletion of either bromodomain with this region caused a partial loss of activity, and deletion of both bromodomains caused greater but incomplete loss of activity. Kinase activity was seen in protein purified from E. coli or from insect Sf9 cells, and survived an in-gel kinase assay after denaturation and renaturation. BRD4 phosphorylated Ser2 of the RNA polymerase C-terminal domain, with a pH profile that was distinct from other Ser2 kinases, and which was insensitive to CDK inhibitors.

	====References====		====References====
	<biblio>		<biblio>
	#Bisgrove pmid=17690245		#Bisgrove pmid=17690245
		+	#Devaiah pmid=22509028
	#Zhou pmid=18971272		#Zhou pmid=18971272
	#Denis pmid=8595877		#Denis pmid=8595877
		+	#Sawa pmid=15143168
	</biblio>		</biblio>

Kinase Family GAPDH

2012-05-09T21:18:07Z

← Older revision		Revision as of 21:18, 9 May 2012
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	The glycolytic enzyme, Glyceraldehyde-3-phosphate dehydrogenase has been demonstrated to have a kinase activity towards viral proteins, a GABA receptor, and in vitro.		The glycolytic enzyme, Glyceraldehyde-3-phosphate dehydrogenase has been demonstrated to have a kinase activity towards viral proteins, a GABA receptor, and in vitro.

-	====Evidence for Protein Kinase Activity=====	+	====Evidence for Protein Kinase Activity====
-	GAPDH from rabbit muscle was reported to autophorphorylate and transphosphorylate <cite>Kawamoto</cite>. ~~The autophosphorylated form~~ appeared to ~~be an intermediate in transphosphorylation -~~ the ~~same~~ phosphate ~~was~~ used ~~for both <check!~~)	+	GAPDH from rabbit muscle was reported to autophorphorylate and transphosphorylate two uncharacterized proteins <cite>Kawamoto</cite>. Transphosphorylation appeared to involve transfer of the phosphate originally used to autophosphorylate, using ATP as a donor. The pH lability profile of the autophosphorylated form suggested the presence of an acyl phosphate (probably phosphorylation of carboxylic acid) rather than the typical ester phosphates of Ser/Thr/Tyr phosphorylation.

-	GAPDH has a kinase function during glycolysis: it first oxidizes glyceraldehyde 3-phosphate, converting the aldehyde group to a carboxylic acid, and then adds inorganic phosphate to the alcohol group of that carboxylic acid [http://en.wikipedia.org/wiki/Glyceraldehyde_3-phosphate_dehydrogenase Wikipedia]. GAPDH uses the energy from the first reaction to drive the unusual, and energetically unfavorable, phosphorylation with inorganic phosphate. The next step in glycolysis inovlves phosphoglycerate kinase acting as a form of phosphatase or reverse kinase: it removes one of the phosphates on the glyceraldehyde diphosphate by converting ADP to ATP.	+	GAPDH has a kinase function during glycolysis: it first oxidizes glyceraldehyde 3-phosphate, converting the aldehyde group to a carboxylic acid, and then adds inorganic phosphate to the alcohol group of that carboxylic acid ([http://en.wikipedia.org/wiki/Glyceraldehyde_3-phosphate_dehydrogenase Wikipedia]). GAPDH uses the energy from the first reaction to drive the unusual, and energetically unfavorable, phosphorylation with inorganic phosphate. The next step in glycolysis inovlves phosphoglycerate kinase acting as a form of phosphatase or reverse kinase: it removes one of the phosphates on the glyceraldehyde diphosphate by converting ADP to ATP.

	HBV: <cite>Duclos-Vallee</cite>		HBV: <cite>Duclos-Vallee</cite>

Kinase Family BRD

2012-05-09T21:13:33Z

New page

__NOTOC__
[[kinase classification|Kinase Classification]]: [[Kinase_Group_SAPPK|Group SAPPK]]: [[Kinase_Family_BRD|Family BRD]]

The BRD (Bromodomain) proteins have twin bromodomains, are chromatin associated, and have been reported to act as protein kinases on the C-terminal domain (CTD) of RNA polymerase.

====Domain Structure====
BRD proteins have twin bromodomains on the N-terminus and a C-terminus of about equal length that has no known domains.

====Evolution====
Mammals have four BRDs (BRD2/RING3, BRD3, BRD4 and BRDT), Drosophila has one (fs(1)h) and C. elegans has 3. A more distantly related homolog is found in fungi (S. cerevisiae Bdf1 and homologs) but that may not be truly orthologous, as others have reported that to be a homolog of Taf1. Other BRD proteins are found across many eukaryotes.

====Evidence for Protein Kinase Activity====
Human BRD2 was first identified as an autophosphorylating nuclear-specific protein in Hela extracts <cite>Denis</cite>. Recombinant BRD2 expressed in ''E. coli'' showed in vitro kinase activity. However, the kinase activity was only seen when the purified recombinant protein was first incubated with Hela cell extract and repurified. It was suggested that this incubation could allow BRD2 to be activated by phosphorylation, but it is also possible that this step allowed BRD2 to bind to a human kinase which was then responsible for the observed activity. Recombinant BRD2 purified from COS cells also showed in vitro kinase activity, without pre-incubation.

If the BRD kinase activity is due to a tightly bound kinase, the most likely candidate is CDK9. It is not known if BRD2 binds CDK9, but BRD4, BRDT and the Drosophila homolog, fs(1)h are all reported to bind CDK9, and BRD4 may induce CDK9 phosphorylation <cite>Zhou, Bisgrove</cite>.

BRD contain two bromodomains and a novel conserved C-terminal region, as well as less-conserved regions. None show an obvious similarity to any known kinases. Mutation of a C-terminal lysine (K578A) abolished the activity seen in ''E. coli'', implicating it either in cryptic kinase activity or binding to an active human kinase.

====References====
<biblio>
#Bisgrove pmid=17690245
#Zhou pmid=18971272
#Denis pmid=8595877
</biblio>

Kinase Group SAPPK

2012-05-09T16:05:26Z

← Older revision		Revision as of 16:05, 9 May 2012
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	====[[Kinase_Family_BCR\|BCR]] ====		====[[Kinase_Family_BCR\|BCR]] ====
	Best known as the fusion partner of the Abl kinase in chronic myologenous leukemia, BCR itself has repeatedly shown kinase activity in immunoprecipitated samples.		Best known as the fusion partner of the Abl kinase in chronic myologenous leukemia, BCR itself has repeatedly shown kinase activity in immunoprecipitated samples.
		+
		+	====[[Kinase_Family_BRD\|BRD]]: Bromodomain Kinases====
		+	This family of dual-bromodomain proteins have been reported as RNA polymerase C-terminal domain kinases.

	====[[Kinase_Family_FASTK\|FASTK]]====		====[[Kinase_Family_FASTK\|FASTK]]====
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	Copines are found in most eukaryotes, with nine members in human. They have twin C2 domains and a VWA domain that has a Rossman fold (a possible nucleotide binding fold). Copines interact with phospholipids in a calcium-dependent manner. A single paper <cite>Caudell</cite> demonstrated kinase activity in human Copine 3. Protein was immunoprecipitated or affinity purified from human cells and found to phosphorylate MBP in both solution and in-gel assays. Tagged protein, affinity purified from yeast also had activity, but E. coli-expressed protein did not. The same antibody (a polyclonal against an 18-AA C-terminal peptide) was used both for pulldown and affinity purification, and showed one contaminating band, at 70kDa. The specific activity was low (estimated as fmol/min/mg). This low rate, the presence of a contaminating band in the immunopreciptates and lack of kinase activity when purified from E. coli are suggestive of the kinase activity being due to a co-purified kinase. However, it is possible that the low activity and lack of E. coli activity are due to a lack of proper folding (the coli extract was largely insoluble), a required posttranslational modification or a (non-kinase) activating subunit. CPNE3 also specifically binds Y1248-phosphorylated ErbB2 <cite>Heinrich</cite>, through phospho-Y1248 and to be required for ErbB2 activation of Src in some circumstances. It also colocalizes with FAK and is upregulated in ErbB2-amplified tumors. The related CPNE1 was shown in high-throughput interaction screens to bind MEK1 (MAP2K1) and phosphatase PPP5C <cite>Tomsig</cite>, suggesting MEK1 as a potential contaminating kinase.		Copines are found in most eukaryotes, with nine members in human. They have twin C2 domains and a VWA domain that has a Rossman fold (a possible nucleotide binding fold). Copines interact with phospholipids in a calcium-dependent manner. A single paper <cite>Caudell</cite> demonstrated kinase activity in human Copine 3. Protein was immunoprecipitated or affinity purified from human cells and found to phosphorylate MBP in both solution and in-gel assays. Tagged protein, affinity purified from yeast also had activity, but E. coli-expressed protein did not. The same antibody (a polyclonal against an 18-AA C-terminal peptide) was used both for pulldown and affinity purification, and showed one contaminating band, at 70kDa. The specific activity was low (estimated as fmol/min/mg). This low rate, the presence of a contaminating band in the immunopreciptates and lack of kinase activity when purified from E. coli are suggestive of the kinase activity being due to a co-purified kinase. However, it is possible that the low activity and lack of E. coli activity are due to a lack of proper folding (the coli extract was largely insoluble), a required posttranslational modification or a (non-kinase) activating subunit. CPNE3 also specifically binds Y1248-phosphorylated ErbB2 <cite>Heinrich</cite>, through phospho-Y1248 and to be required for ErbB2 activation of Src in some circumstances. It also colocalizes with FAK and is upregulated in ErbB2-amplified tumors. The related CPNE1 was shown in high-throughput interaction screens to bind MEK1 (MAP2K1) and phosphatase PPP5C <cite>Tomsig</cite>, suggesting MEK1 as a potential contaminating kinase.

-	~~====BRD: Bromodomain Kinases====~~
-	This family consists of the BRD2 (RING3) kinase and homologs in human and model organisms. BRD2 was first identified as an autophosphorylating nuclear-specific protein in Hela extracts <cite>Denis</cite>. Recombinant BRD2 expressed in ''E. coli'' showed in vitro kinase activity. However, the kinase activity was only seen when the purified recombinant protein was first incubated with Hela cell extract and repurified. It was suggested that this incubation could allow BRD2 to be activated by phosphorylation, but it is also possible that this step allowed BRD2 to bind to a human kinase which was then responsible for the observed activity. Recombinant BRD2 purified from COS cells also showed in vitro kinase activity, without pre-incubation.
-
-	If the BRD kinase activity is due to a tightly bound kinase, the most likely candidate is CDK9. It is not known if BRD2 binds CDK9, but BRD4, BRDT and the Drosophila homolog, fs(1)h are all reported to bind CDK9, and BRD4 may induce CDK9 phosphorylation <cite>Zhou, Bisgrove</cite>.
-
-	BRD contain two bromodomains and a novel conserved C-terminal region, as well as less-conserved regions. None show an obvious similarity to any known kinases. Mutation of a C-terminal lysine (K578A) abolished the activity seen in ''E. coli'', implicating it either in cryptic kinase activity or binding to an active human kinase.

	====GTF2F1/TFIIFa====		====GTF2F1/TFIIFa====
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	=== References ===		=== References ===
	<biblio>		<biblio>
-	~~#Bisgrove pmid=17690245~~
	#WSTF pmid=19092802		#WSTF pmid=19092802
	#Brutsche pmid=11207646		#Brutsche pmid=11207646
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	#Nielsen pmid=10562550		#Nielsen pmid=10562550
	#Steussy pmid=11483605		#Steussy pmid=11483605
-	~~#Denis pmid=8595877~~
	#Dikstein pmid=8625415		#Dikstein pmid=8625415
	#Solow pmid=11278496		#Solow pmid=11278496
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	#Tomsig pmid=12522145		#Tomsig pmid=12522145
	#Rossignol pmid=10428810		#Rossignol pmid=10428810
-	~~#Zhou pmid=18971272~~
	#Manning1 pmid=12368087		#Manning1 pmid=12368087
	#Manning2 pmid=12471243		#Manning2 pmid=12471243

User talk:Roland Dunbrack

2012-05-09T16:02:37Z

Welcome!

New page

'''Welcome to ''WikiKinome''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:Gerard|Gerard]] 16:02, 9 May 2012 (UTC)

User:Roland Dunbrack

2012-05-09T16:02:37Z

Creating user page with biography of new user.

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Professor, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia PA

I have a research group in computational structural biology, focusing on structural bioinformatics and methods for protein structure prediction. We are particularly interested in modeling of oligomeric complexes. Our ProtCID website (http://dunbrack2.fccc.edu/protcid) has information on homo- and heterodimeric interactions of proteins observed in multiple crystal forms. The page on kinases (browse the Pfam families for (Pkinase) and (Pkinase_Tyr) have several commonly observed dimer interactions. For instance, the asymmetric EGFR dimer is observed in several EGFR crystals and also Erbb2 and Erbb4.

User:Roland Dunbrack

2012-05-09T16:02:37Z

created new account User:Roland Dunbrack

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