Phosphoglycerate Kinase - Revision history

Michal Harel at 08:38, 10 January 2023

Michal Harel — Tue, 10 Jan 2023 08:38:19 GMT

←Older revision		Revision as of 08:38, 10 January 2023
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	== PGK in the Glycolysis Cycle ==		== PGK in the Glycolysis Cycle ==

-	'''Phosphoglycerate kinase''' is a crucial enzyme in the glycolysis cycle. This cycle is a series of ten reactions which ultimately breaks down glucose into pyruvate while generating 2 NADH and 2 ATP molecules. Phosphoglycerate kinase is the seventh enzyme in the cycle which catalyzes the reaction of 1,3-Biphosphoglycerate and ADP to produce <scene name='Shane_Harmon_Sandbox/Product/2'>3-Phosphoglycerate</scene> and <scene name='Shane_Harmon_Sandbox/Atp/4'>ATP</scene>. This method for ATP production is known as substrate-level phosphorylation because it produces energy storing ATP molecules without the use of oxygen, NADH, or an ATPase. The reaction is highly exergonic allowing it to be coupled with the less thermodynamically favored GADPH reaction of the cycle so both reactions occur spontaneously. See [[Glycolysis Enzymes]].	+	'''Phosphoglycerate kinase''' is a crucial enzyme in the glycolysis cycle. This cycle is a series of ten reactions which ultimately breaks down glucose into pyruvate while generating 2 NADH and 2 ATP molecules. Phosphoglycerate kinase is the seventh enzyme in the cycle which catalyzes the reaction of 1,3-Biphosphoglycerate and ADP to produce <scene name='Shane_Harmon_Sandbox/Product/2'>3-Phosphoglycerate</scene> and <scene name='Shane_Harmon_Sandbox/Atp/4'>ATP</scene>. This method for ATP production is known as substrate-level phosphorylation because it produces energy storing ATP molecules without the use of oxygen, NADH, or an ATPase. The reaction is highly exergonic allowing it to be coupled with the less thermodynamically favored GADPH reaction of the cycle so both reactions occur spontaneously. See [[Glycolysis Enzymes]], [[Gluconeogenesis]].

	== Structure ==		== Structure ==

Michal Harel at 07:45, 18 November 2019

Michal Harel — Mon, 18 Nov 2019 07:45:14 GMT

←Older revision		Revision as of 07:45, 18 November 2019
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	</StructureSection>		</StructureSection>
-
-	==3D structures of phosphoglycerate kinase ==
-
-	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
-	{{#tree:id=OrganizedByTopic\|openlevels=0\|
-
-	*'''Phosphoglycerate kinase'''
-
-	**[[2pgk]] – PGK – horse<br />
-	**[[2p9q]] – mPGK2 – mouse<BR />
-	**[[1fw8]] – yPGK – yeast<BR />
-	**[[3oz7]], [[3oza]] – PfPGK – ''Plasmodium falciparum''<BR />
-	**[[3q3v]] – PGK – ''Campylobacter jejuni''<BR />
-	**[[2ie8]] – PGK – ''Thermus caldophilus''<BR />
-	**[[1zmr]] – PGK – ''Escherichia coli''<BR />
-	**[[1v6s]] – PGK – ''Thermos thermophilus''<BR />
-	**[[3uwd]] - PGK – ''Bacillus anthracis''<br />
-	**[[4dg5]] – PGK – ''Staphylococcus aureus''<br />
-	**[[4ehj]] – FtPGK – ''Francisella tularensis''<br />
-	**[[5bt8]] – PGK – ''Acinetobacter baumannii''<br />
-	**[[6i06]] – PsPGK – ''Pseudomonas''<br />
-
-	*Phosphoglycerate kinase binary complex
-
-	**[[2xe6]], [[3c39]] – hPGK1 + PGA - human<BR />
-	**[[2zgv]] - hPGK1 + ADP<BR />
-	**[[5o7d]], [[5mxm]], [[5m6z]], [[5m3u]], [[5m1r]] – hPGK1 (mutant) + ADP <br />
-	**[[5np8]] – hPGK1 + inhibitor <br />
-	**[[3c3b]], [[3c3c]] - hPGK1 + CDP <br />
-	[[3zoz]] – hPGK1 + Br<br />[[1vjc]] – pPGK + MgATP – pig<BR />
-	**[[1vjd]] - pPGK + ATP<BR />
-	**[[2p9t]] – mPGK2 + PGA<BR />
-	**[[1ltk]] – PfPGK + AMP<BR />
-	**[[16pk]]– TbPGK (mutant) + bisubstrate analog – ''Trypanosoma brucei''<BR />
-	**[[1php]] – PGK + ADP – ''Geobacillus stearothermophilus''<BR />
-	**[[4fey]] – FtPGK + ADP<br />
-	**[[1vpe]] – PGK + ANP – ''Thermotoga maritima''<BR />
-	**[[2cun]] – PGK + PGA – ''Pyrococcus horikoshii''<BR />
-	**[[3zlb]] - PGK + ANP – ''Streptococcus pneumoniae''<br />
-	**[[4ng4]] – PGK + ADP – ''Coxiella burnetii''<br />
-	**[[6hxe]] – PsPGK + 3PG <br />
-
-	*Phosphoglycerate kinase ternary complex
-
-	**[[2paa]] - mPGK2 + ATP + PGA<BR />
-	**[[1hdi]] - mPGK + MgATP + PGA<BR />
-	**[[1kf0]] - mPGK + AMPPCP + PGA<BR />
-	**[[1qpg]] - yPGK + MgATP + PGA<BR />
-	**[[3pgk]] - yPGK + ATP + PGA<BR />
-	**[[13pk]] - TbPGK + ADP + PGA<BR />
-	**[[2y3i]], [[2ybe]], [[2xe7]], [[2x13]], [[3c3a]] – hPGK1 + ADP + PGA <BR />
-	**[[2x15]] - hPGK1 + bisphosphoglycerate + ADP<br />
-	**[[2xe8]] - hPGK1 + AMPPNP + PGA<BR />
-	**[[2x14]] - hPGK1 (mutant) + AMPPCP + PGA<BR />
-	**[[2wzb]] - hPGK1 + ADP + MgF3 + PGA<BR />
-	**[[4axx]] - hPGK1 + ADP + BeF3 + 3PG<br />
-	**[[4o33]] - hPGK1 + terazosin + 3PG<br />
-	**[[2wzc]] - hPGK1 + ADP + AlF4 + PGA<BR />
-	**[[2wzd]] - hPGK1 (mutant) + ADP + AlF3 + PGA<BR />
-	**[[2paa]] - mPGK2 + ATP + PGA<BR />
-	**[[1hdi]] - mPGK + MgATP + PGA<BR />
-	**[[1kf0]] - mPGK + AMPPCP + PGA<BR />
-	**[[4o3f]] - mPGK1 + terazosin + 3PG<br />
-	**[[1qpg]] - yPGK + MgATP + PGA<BR />
-	**[[3pgk]] - yPGK + ATP + PGA<BR />
-	**[[13pk]] - TbPGK + ADP + PGA<BR />
-	}}
-
-
-
-
-

	==Additional Resources==		==Additional Resources==

Michal Harel at 07:44, 18 November 2019

Michal Harel — Mon, 18 Nov 2019 07:44:08 GMT

←Older revision		Revision as of 07:44, 18 November 2019
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	*'''Phosphoglycerate kinase'''		*'''Phosphoglycerate kinase'''

		+	**[[2pgk]] – PGK – horse<br />
		+	**[[2p9q]] – mPGK2 – mouse<BR />
		+	**[[1fw8]] – yPGK – yeast<BR />
	**[[3oz7]], [[3oza]] – PfPGK – ''Plasmodium falciparum''<BR />		**[[3oz7]], [[3oza]] – PfPGK – ''Plasmodium falciparum''<BR />
	**[[3q3v]] – PGK – ''Campylobacter jejuni''<BR />		**[[3q3v]] – PGK – ''Campylobacter jejuni''<BR />
-	**[[2p9q]] – mPGK2 – mouse<BR />
	**[[2ie8]] – PGK – ''Thermus caldophilus''<BR />		**[[2ie8]] – PGK – ''Thermus caldophilus''<BR />
	**[[1zmr]] – PGK – ''Escherichia coli''<BR />		**[[1zmr]] – PGK – ''Escherichia coli''<BR />
	**[[1v6s]] – PGK – ''Thermos thermophilus''<BR />		**[[1v6s]] – PGK – ''Thermos thermophilus''<BR />
-	**[[1fw8]] – yPGK – yeast<BR />
-	**[[2pgk]] – PGK – horse<br />
	**[[3uwd]] - PGK – ''Bacillus anthracis''<br />		**[[3uwd]] - PGK – ''Bacillus anthracis''<br />
	**[[4dg5]] – PGK – ''Staphylococcus aureus''<br />		**[[4dg5]] – PGK – ''Staphylococcus aureus''<br />
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	*Phosphoglycerate kinase binary complex		*Phosphoglycerate kinase binary complex

-	**[[1vjc]] – pPGK + MgATP – pig<BR />	+	**[[2xe6]], [[3c39]] – hPGK1 + PGA - human<BR />
		+	**[[2zgv]] - hPGK1 + ADP<BR />
		+	**[[5o7d]], [[5mxm]], [[5m6z]], [[5m3u]], [[5m1r]] – hPGK1 (mutant) + ADP <br />
		+	**[[5np8]] – hPGK1 + inhibitor <br />
		+	**[[3c3b]], [[3c3c]] - hPGK1 + CDP <br />
		+	[[3zoz]] – hPGK1 + Br<br />[[1vjc]] – pPGK + MgATP – pig<BR />
	**[[1vjd]] - pPGK + ATP<BR />		**[[1vjd]] - pPGK + ATP<BR />
		+	**[[2p9t]] – mPGK2 + PGA<BR />
	**[[1ltk]] – PfPGK + AMP<BR />		**[[1ltk]] – PfPGK + AMP<BR />
	**[[16pk]]– TbPGK (mutant) + bisubstrate analog – ''Trypanosoma brucei''<BR />		**[[16pk]]– TbPGK (mutant) + bisubstrate analog – ''Trypanosoma brucei''<BR />
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	**[[1vpe]] – PGK + ANP – ''Thermotoga maritima''<BR />		**[[1vpe]] – PGK + ANP – ''Thermotoga maritima''<BR />
	**[[2cun]] – PGK + PGA – ''Pyrococcus horikoshii''<BR />		**[[2cun]] – PGK + PGA – ''Pyrococcus horikoshii''<BR />
-	**[[2p9t]] – mPGK2 + PGA<BR />
-	**[[2xe6]], [[3c39]] – hPGK1 + PGA - human<BR />
-	**[[2zgv]] - hPGK1 + ADP<BR />
-	**[[5o7d]], [[5mxm]], [[5m6z]], [[5m3u]], [[5m1r]] – hPGK1 (mutant) + ADP <br />
-	**[[5np8]] – hPGK1 + inhibitor <br />
-	**[[3c3b]], [[3c3c]] - hPGK1 + CDP <br />
-	**[[3zoz]] – hPGK1 + Br<br />
	**[[3zlb]] - PGK + ANP – ''Streptococcus pneumoniae''<br />		**[[3zlb]] - PGK + ANP – ''Streptococcus pneumoniae''<br />
	**[[4ng4]] – PGK + ADP – ''Coxiella burnetii''<br />		**[[4ng4]] – PGK + ADP – ''Coxiella burnetii''<br />
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	**[[4axx]] - hPGK1 + ADP + BeF3 + 3PG<br />		**[[4axx]] - hPGK1 + ADP + BeF3 + 3PG<br />
	**[[4o33]] - hPGK1 + terazosin + 3PG<br />		**[[4o33]] - hPGK1 + terazosin + 3PG<br />
-	**[[4o3f]] - mPGK1 + terazosin + 3PG<br />
	**[[2wzc]] - hPGK1 + ADP + AlF4 + PGA<BR />		**[[2wzc]] - hPGK1 + ADP + AlF4 + PGA<BR />
	**[[2wzd]] - hPGK1 (mutant) + ADP + AlF3 + PGA<BR />		**[[2wzd]] - hPGK1 (mutant) + ADP + AlF3 + PGA<BR />
		+	**[[2paa]] - mPGK2 + ATP + PGA<BR />
		+	**[[1hdi]] - mPGK + MgATP + PGA<BR />
		+	**[[1kf0]] - mPGK + AMPPCP + PGA<BR />
		+	**[[4o3f]] - mPGK1 + terazosin + 3PG<br />
		+	**[[1qpg]] - yPGK + MgATP + PGA<BR />
		+	**[[3pgk]] - yPGK + ATP + PGA<BR />
		+	**[[13pk]] - TbPGK + ADP + PGA<BR />
	}}		}}

Michal Harel at 07:34, 18 November 2019

Michal Harel — Mon, 18 Nov 2019 07:34:11 GMT

←Older revision		Revision as of 07:34, 18 November 2019
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	Recent study of PGK has revolved around its function in tumor formation and growth. It has been shown that in addition to catalyzing its normal reaction of 1,3-Biphosphoglycerate and ADP to ATP and 3-Phosphoglycerate, PGK can also function to cleave disulfide bonds. Specifically, the review of sulfide bond cleavage indicates PGK has been shown to cleave disulfide bonds in the protein zymogen plasmin to produce the active form of the protein. The active form of plasmin is responsible for angiogenesis or blood vessel formation in tumors<ref>PMID:12189052</ref> Without the formation of blood vessels in tumors, nutrients are limited and tumor growth is therfore limited. Once blood vessels are established growth can rapidly increase. The fact that tumor cells secrete PGK to allow blood vessel formation through the activation of the zymogen plasmin has important implications for understanding its regulation. If the regulation of PGK in tumor cells can be understood, it might be possible to inhibit the overproduction and secretion of PGK to limit angiogenesis in tumors.		Recent study of PGK has revolved around its function in tumor formation and growth. It has been shown that in addition to catalyzing its normal reaction of 1,3-Biphosphoglycerate and ADP to ATP and 3-Phosphoglycerate, PGK can also function to cleave disulfide bonds. Specifically, the review of sulfide bond cleavage indicates PGK has been shown to cleave disulfide bonds in the protein zymogen plasmin to produce the active form of the protein. The active form of plasmin is responsible for angiogenesis or blood vessel formation in tumors<ref>PMID:12189052</ref> Without the formation of blood vessels in tumors, nutrients are limited and tumor growth is therfore limited. Once blood vessels are established growth can rapidly increase. The fact that tumor cells secrete PGK to allow blood vessel formation through the activation of the zymogen plasmin has important implications for understanding its regulation. If the regulation of PGK in tumor cells can be understood, it might be possible to inhibit the overproduction and secretion of PGK to limit angiogenesis in tumors.
		+
		+	==3D structures of phosphoglycerate kinase ==
		+	[[Phosphoglycerate kinase 3D structures]]
		+
	</StructureSection>		</StructureSection>

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	**[[4ehj]] – FtPGK – ''Francisella tularensis''<br />		**[[4ehj]] – FtPGK – ''Francisella tularensis''<br />
	**[[5bt8]] – PGK – ''Acinetobacter baumannii''<br />		**[[5bt8]] – PGK – ''Acinetobacter baumannii''<br />
		+	**[[6i06]] – PsPGK – ''Pseudomonas''<br />

	*Phosphoglycerate kinase binary complex		*Phosphoglycerate kinase binary complex
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	**[[3zlb]] - PGK + ANP – ''Streptococcus pneumoniae''<br />		**[[3zlb]] - PGK + ANP – ''Streptococcus pneumoniae''<br />
	**[[4ng4]] – PGK + ADP – ''Coxiella burnetii''<br />		**[[4ng4]] – PGK + ADP – ''Coxiella burnetii''<br />
		+	**[[6hxe]] – PsPGK + 3PG <br />

	*Phosphoglycerate kinase ternary complex		*Phosphoglycerate kinase ternary complex

Alexander Berchansky at 12:30, 1 August 2019

Alexander Berchansky — Thu, 01 Aug 2019 12:30:52 GMT

←Older revision		Revision as of 12:30, 1 August 2019
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	PGK structure shows an open-to-close transition upon hinge bending. PG assumes the open conformation upon release of PGA and ATP. The closed conformation active site contains PGA, ADP and AlF<sub>4</sub>-1 ion which mimics the phosphate ion<ref>PMID:21549713</ref>.		PGK structure shows an open-to-close transition upon hinge bending. PG assumes the open conformation upon release of PGA and ATP. The closed conformation active site contains PGA, ADP and AlF<sub>4</sub>-1 ion which mimics the phosphate ion<ref>PMID:21549713</ref>.
-	*<scene name='38/387911/Cv/2'>Phosphoglycerate binding site</scene>.	+	*<scene name='38/387911/Cv/10'>Phosphoglycerate binding site</scene>.
-	*<scene name='38/387911/Cv/4'>AlF4- binding site</scene>.	+	*<scene name='38/387911/Cv/11'>AlF4- binding site</scene>.
-	*<scene name='38/387911/Cv/7'>ADP binding site</scene>.	+	*<scene name='38/387911/Cv/12'>ADP binding site</scene>.
-	*<scene name='38/387911/Cv/9'>Whole binding site</scene>. Water molecules shown as red spheres.	+	*<scene name='38/387911/Cv/13'>Whole binding site</scene>. Water molecules are shown as red spheres.

	== Reaction Mechanism ==		== Reaction Mechanism ==

Joel L. Sussman at 10:02, 24 August 2018

Joel L. Sussman — Fri, 24 Aug 2018 10:02:06 GMT

←Older revision		Revision as of 10:02, 24 August 2018
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	== Kinetics ==		== Kinetics ==

-	Given that Phosphoglycerate kinase is a monomeric protein standard Michealis-Menton kinetics would be expected; however, this is not the case. Multiple experiments have shown that the data, when transformed into either double-reciprocal or Eadie-Hofstee plots is non-linear; Eadie-Hofstee plots curve upward. One possible explanation for the non-linearity, negative cooperativity, is ruled out because PGK does not have multiple subunits. In one study that conducted kinetic tests with a 1000 fold range of substrates, at the highest concentrations of substrate the rate was still increasing; this puts the Km value in the 2-5mM range <ref>PMID:348474 </ref>. Recently, a new model was proposed to explain this conflict between the seemingly negative cooperative kinetics and the monomeric structure of PGK. The enzyme may form a complex with the metabolic enzyme glyceraldehyde-3-phosphate dehydrogenase. This multi-subunit complex would be capable of the negative cooperativity that is indicated by the non-linear kinetics of PGK.<ref> ~~Macioszek, Jerzy et al. 1990. Kinetics of the Two-Enzyme Phosphoglycerate Kinase/Glyceraldehyde-3-Phosphate Dehydrogenase Couple. Plant Physiology 94~~: ~~291-296.~~</ref>.	+	Given that Phosphoglycerate kinase is a monomeric protein standard Michealis-Menton kinetics would be expected; however, this is not the case. Multiple experiments have shown that the data, when transformed into either double-reciprocal or Eadie-Hofstee plots is non-linear; Eadie-Hofstee plots curve upward. One possible explanation for the non-linearity, negative cooperativity, is ruled out because PGK does not have multiple subunits. In one study that conducted kinetic tests with a 1000 fold range of substrates, at the highest concentrations of substrate the rate was still increasing; this puts the Km value in the 2-5mM range <ref>PMID:348474 </ref>. Recently, a new model was proposed to explain this conflict between the seemingly negative cooperative kinetics and the monomeric structure of PGK. The enzyme may form a complex with the metabolic enzyme glyceraldehyde-3-phosphate dehydrogenase. This multi-subunit complex would be capable of the negative cooperativity that is indicated by the non-linear kinetics of PGK<ref>PMID:16667700 </ref>.

	== Regulation ==		== Regulation ==

Joel L. Sussman at 10:00, 24 August 2018

Joel L. Sussman — Fri, 24 Aug 2018 10:00:42 GMT

←Older revision		Revision as of 10:00, 24 August 2018
Line 28:		Line 28:
	== Kinetics ==		== Kinetics ==

-	Given that Phosphoglycerate kinase is a monomeric protein standard Michealis-Menton kinetics would be expected; however, this is not the case. Multiple experiments have shown that the data, when transformed into either double-reciprocal or Eadie-Hofstee plots is non-linear; Eadie-Hofstee plots curve upward. One possible explanation for the non-linearity, negative cooperativity, is ruled out because PGK does not have multiple subunits. In one study that conducted kinetic tests with a 1000 fold range of substrates, at the highest concentrations of substrate the rate was still increasing; this puts the Km value in the 2-5mM range <ref> ~~Scopes, Robert. 1977. The Steady State Kinetics of Yeast Phosphoglycerate Kinase. European Journal of Biochemistry. 85, 503-516~~ </ref> Recently, a new model was proposed to explain this conflict between the seemingly negative cooperative kinetics and the monomeric structure of PGK. The enzyme may form a complex with the metabolic enzyme glyceraldehyde-3-phosphate dehydrogenase. This multi-subunit complex would be capable of the negative cooperativity that is indicated by the non-linear kinetics of PGK.<ref> Macioszek, Jerzy et al. 1990. Kinetics of the Two-Enzyme Phosphoglycerate Kinase/Glyceraldehyde-3-Phosphate Dehydrogenase Couple. Plant Physiology 94: 291-296.</ref>.	+	Given that Phosphoglycerate kinase is a monomeric protein standard Michealis-Menton kinetics would be expected; however, this is not the case. Multiple experiments have shown that the data, when transformed into either double-reciprocal or Eadie-Hofstee plots is non-linear; Eadie-Hofstee plots curve upward. One possible explanation for the non-linearity, negative cooperativity, is ruled out because PGK does not have multiple subunits. In one study that conducted kinetic tests with a 1000 fold range of substrates, at the highest concentrations of substrate the rate was still increasing; this puts the Km value in the 2-5mM range <ref>PMID:348474 </ref>. Recently, a new model was proposed to explain this conflict between the seemingly negative cooperative kinetics and the monomeric structure of PGK. The enzyme may form a complex with the metabolic enzyme glyceraldehyde-3-phosphate dehydrogenase. This multi-subunit complex would be capable of the negative cooperativity that is indicated by the non-linear kinetics of PGK.<ref> Macioszek, Jerzy et al. 1990. Kinetics of the Two-Enzyme Phosphoglycerate Kinase/Glyceraldehyde-3-Phosphate Dehydrogenase Couple. Plant Physiology 94: 291-296.</ref>.

	== Regulation ==		== Regulation ==

Joel L. Sussman at 09:57, 24 August 2018

Joel L. Sussman — Fri, 24 Aug 2018 09:57:34 GMT

←Older revision		Revision as of 09:57, 24 August 2018
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	== Other Functions ==		== Other Functions ==

-	Recent study of PGK has revolved around its function in tumor formation and growth. It has been shown that in addition to catalyzing its normal reaction of 1,3-Biphosphoglycerate and ADP to ATP and 3-Phosphoglycerate, PGK can also function to cleave disulfide bonds. Specifically, the review of sulfide bond cleavage indicates PGK has been shown to cleave disulfide bonds in the protein zymogen plasmin to produce the active form of the protein. The active form of plasmin is responsible for angiogenesis or blood vessel formation in tumors <ref> ~~Hogg, PJ. 2002. Biological Regulation through protein disulfide bond cleavage. Redox Report. 7(2), 71-77.~~ </ref> Without the formation of blood vessels in tumors, nutrients are limited and tumor growth is therfore limited. Once blood vessels are established growth can rapidly increase. The fact that tumor cells secrete PGK to allow blood vessel formation through the activation of the zymogen plasmin has important implications for understanding its regulation. If the regulation of PGK in tumor cells can be understood, it might be possible to inhibit the overproduction and secretion of PGK to limit angiogenesis in tumors.	+	Recent study of PGK has revolved around its function in tumor formation and growth. It has been shown that in addition to catalyzing its normal reaction of 1,3-Biphosphoglycerate and ADP to ATP and 3-Phosphoglycerate, PGK can also function to cleave disulfide bonds. Specifically, the review of sulfide bond cleavage indicates PGK has been shown to cleave disulfide bonds in the protein zymogen plasmin to produce the active form of the protein. The active form of plasmin is responsible for angiogenesis or blood vessel formation in tumors<ref>PMID:12189052</ref> Without the formation of blood vessels in tumors, nutrients are limited and tumor growth is therfore limited. Once blood vessels are established growth can rapidly increase. The fact that tumor cells secrete PGK to allow blood vessel formation through the activation of the zymogen plasmin has important implications for understanding its regulation. If the regulation of PGK in tumor cells can be understood, it might be possible to inhibit the overproduction and secretion of PGK to limit angiogenesis in tumors.
	</StructureSection>		</StructureSection>

Joel L. Sussman at 09:56, 24 August 2018

Joel L. Sussman — Fri, 24 Aug 2018 09:56:03 GMT

←Older revision		Revision as of 09:56, 24 August 2018
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	== Regulation ==		== Regulation ==

-	The role of PGK in glycolysis is very important for the production of ATP through substrate level phosphorylation. Regulation of this protein is thereby controlled by ATP or energy level of the cell. Recent research in frogs which can withstand freezing temperatures indicates that PGK is up regulated by the cold and more specifically by low levels of oxygen <ref> ~~Shaobo, Wu et al. 2009. PGK1 expression responds to freezing, anoxia, and dehydration stresses in freeze tolerant wood frog, Rana sylvatica. Journal of Experimental Zoology. 311, 57-67~~ </ref> This makes logical sense as when oxygen is low, oxidative phosphorylation cannot occur. Thus without oxygen and oxidative phosphorylation, ATP levels begin to drop. In response to decreased ATP, PGK is up regulated to increase the amount of ATP produced by substrate level phosphorylation. It could therefore also be expected that ADP might act to inhibit or down regulated PGK expression.	+	The role of PGK in glycolysis is very important for the production of ATP through substrate level phosphorylation. Regulation of this protein is thereby controlled by ATP or energy level of the cell. Recent research in frogs which can withstand freezing temperatures indicates that PGK is up regulated by the cold and more specifically by low levels of oxygen<ref>PMID:18785212 </ref>. This makes logical sense as when oxygen is low, oxidative phosphorylation cannot occur. Thus without oxygen and oxidative phosphorylation, ATP levels begin to drop. In response to decreased ATP, PGK is up regulated to increase the amount of ATP produced by substrate level phosphorylation. It could therefore also be expected that ADP might act to inhibit or down regulated PGK expression.

	== Other Functions ==		== Other Functions ==

Joel L. Sussman at 09:54, 24 August 2018

Joel L. Sussman — Fri, 24 Aug 2018 09:54:24 GMT

←Older revision		Revision as of 09:54, 24 August 2018
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	The bilobed structure of PGK is very crucial in its catalytic function. The active site is broken into two pieces, one on the interior of each lobe or domain. The N-terminal domain has a basic region where the 1,3-Biphosphoglycerate and 3-phosphoglycerate bind while the C-terminal domain has the binding sites for the nucleotide substrates, ADP and ATP. Upon binding of both substrate molecules at the active sites, the protein’s conformation changes such that the two lobes of the protein swing together <ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. 499 </ref> When the two domains swing shut, a hydrophobic chamber free from water is established where the reaction can take place. This hydrophobic chamber is necessary to prevent ATP hydrolysis <ref name="Auer" /> The hinge for this conformational change is beta sheet L and the new conformation is formed via a salt bridge between <scene name='Shane_Harmon_Sandbox/Arg_and_asp/2'>Arg 62 and Asp 200</scene> <ref>PMID:6115427</ref> Recent research indicates that the mechanism for closure of the two domains is a series of hydrogen bond interactions that occur upon binding of the substrates on both domains <ref>PMID:20088776 </ref>		The bilobed structure of PGK is very crucial in its catalytic function. The active site is broken into two pieces, one on the interior of each lobe or domain. The N-terminal domain has a basic region where the 1,3-Biphosphoglycerate and 3-phosphoglycerate bind while the C-terminal domain has the binding sites for the nucleotide substrates, ADP and ATP. Upon binding of both substrate molecules at the active sites, the protein’s conformation changes such that the two lobes of the protein swing together <ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. 499 </ref> When the two domains swing shut, a hydrophobic chamber free from water is established where the reaction can take place. This hydrophobic chamber is necessary to prevent ATP hydrolysis <ref name="Auer" /> The hinge for this conformational change is beta sheet L and the new conformation is formed via a salt bridge between <scene name='Shane_Harmon_Sandbox/Arg_and_asp/2'>Arg 62 and Asp 200</scene> <ref>PMID:6115427</ref> Recent research indicates that the mechanism for closure of the two domains is a series of hydrogen bond interactions that occur upon binding of the substrates on both domains <ref>PMID:20088776 </ref>

-	The mechanism of catalysis has not been fully established because the PGK/1-3biphophoglycerate complex is highly unstable; however, it is thought that the mechanism is similar to that of hexokinase. Hexokinase catalyzes the removal of a phosphate group from ATP to glucose and has a very similar structure and conformational change via a hinge. PGK has a similar function except it catalyzes the transfer of a phosphate to form ATP instead of using ATP. The reaction of PGK removes the C1 phosphate group from 1,3-biphosphoglycerate and transfers it to ADP to form ATP. Once the substrates bind to the active sites, the protein domains swing shut forcing the substrates into correct position for the reaction to proceed <ref>~~Harnan, G. et al. 1992. Domain Motions in Phosphoglycerate Kinase~~: ~~Determination of Interdomain Distance Distribution by Site Specific Labeling and Time Resolved Flourescense Energy Transfer. PNAS. 89:11764-11768.~~</ref>	+	The mechanism of catalysis has not been fully established because the PGK/1-3biphophoglycerate complex is highly unstable; however, it is thought that the mechanism is similar to that of hexokinase. Hexokinase catalyzes the removal of a phosphate group from ATP to glucose and has a very similar structure and conformational change via a hinge. PGK has a similar function except it catalyzes the transfer of a phosphate to form ATP instead of using ATP. The reaction of PGK removes the C1 phosphate group from 1,3-biphosphoglycerate and transfers it to ADP to form ATP. Once the substrates bind to the active sites, the protein domains swing shut forcing the substrates into correct position for the reaction to proceed<ref>PMID:1465395 </ref>.

	The general mechanism is a single displacement Sn2 reaction in which the ADP-B-phosphate oxygen atom initiates nucleophilic attack on the 1-phosphate group of 1-3biphosphoglycerate <ref name="Auer" />. Thus, the phosphoryl group is transferred directly via a charged transition state. The product, ATP, is favored because it's negatively charged oxygens of the 3 phosphates form <scene name='Shane_Harmon_Sandbox/Atp/5'>hydrogen bonds</scene> with the enzyme. The 3 hydrogen bonds of ATP are favored over the 2 hydrogen bonds of ADP.		The general mechanism is a single displacement Sn2 reaction in which the ADP-B-phosphate oxygen atom initiates nucleophilic attack on the 1-phosphate group of 1-3biphosphoglycerate <ref name="Auer" />. Thus, the phosphoryl group is transferred directly via a charged transition state. The product, ATP, is favored because it's negatively charged oxygens of the 3 phosphates form <scene name='Shane_Harmon_Sandbox/Atp/5'>hydrogen bonds</scene> with the enzyme. The 3 hydrogen bonds of ATP are favored over the 2 hydrogen bonds of ADP.