Sandbox Reserved 470: Difference between revisions
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==Introduction== | ==Introduction== | ||
---- | ---- | ||
'''[[Glyceraldehyde-3-phosphate Dehydrogenase]]''' | *'''[[Glyceraldehyde-3-phosphate Dehydrogenase]]''' | ||
<Structure load='3gpd' size='350' frame='true' align='right' caption='Glyceraldehyde-3-phosphate Dehydrogenase' scene='Insert optional scene name here' />(abbreviated as GAPDH or the less common G3PDH) (EC 1.2.1.12) ~37kDa is a well-known [http://en.wikipedia.org/wiki/Enzyme enzyme] which catalyzes the sixth step of [[glycolysis]], a reversible cytosolic process in [http://en.wikipedia.org/wiki/Eukaryote eukaryotes] which involves the breakdown of glucose for energy and carbon molecules. Along with its role in glycolysis and [http://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], recent research has determined that GAPDH is actually a multifunctional protein, as it has numerous defined, non-metabolic functions involved in multiple subcellular processes including [http://en.wikipedia.org/wiki/Transcription transcription] activation, ER to Golgi transportation, transcriptional control of histone [http://en.wikipedia.org/wiki/Gene_Expression gene expression], nuclear membrane fusion, neuronal initiation of [http://en.wikipedia.org/wiki/Apoptosis apoptosis], recognizing fraudulently incorporated nucleotides in DNA, and maintaining [http://en.wikipedia.org/wiki/Telomere telomere] structures. Research also shows that it possibly has a direct involvement in cellular phenotype of human [http://en.wikipedia.org/wiki/Neurodegeneration neurodegenerative] disorders, especially those characterized by expansion of [http://en.wikipedia.org/wiki/CAG_Triplet_Repeat_Disorders CAG repeats]. | <Structure load='3gpd' size='350' frame='true' align='right' caption='Glyceraldehyde-3-phosphate Dehydrogenase' scene='Insert optional scene name here' />(abbreviated as GAPDH or the less common G3PDH) (EC 1.2.1.12) ~37kDa is a well-known [http://en.wikipedia.org/wiki/Enzyme enzyme] which catalyzes the sixth step of [[glycolysis]], a reversible cytosolic process in [http://en.wikipedia.org/wiki/Eukaryote eukaryotes] which involves the breakdown of glucose for energy and carbon molecules. Along with its role in glycolysis and [http://en.wikipedia.org/wiki/Gluconeogenesis gluconeogenesis], recent research has determined that GAPDH is actually a multifunctional protein, as it has numerous defined, non-metabolic functions involved in multiple subcellular processes including [http://en.wikipedia.org/wiki/Transcription transcription] activation, ER to Golgi transportation, transcriptional control of histone [http://en.wikipedia.org/wiki/Gene_Expression gene expression], nuclear membrane fusion, neuronal initiation of [http://en.wikipedia.org/wiki/Apoptosis apoptosis], recognizing fraudulently incorporated nucleotides in DNA, and maintaining [http://en.wikipedia.org/wiki/Telomere telomere] structures. Research also shows that it possibly has a direct involvement in cellular phenotype of human [http://en.wikipedia.org/wiki/Neurodegeneration neurodegenerative] disorders, especially those characterized by expansion of [http://en.wikipedia.org/wiki/CAG_Triplet_Repeat_Disorders CAG repeats]. | ||
==Structure== | ==Structure== | ||
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==Importance== | ==Importance== | ||
---- | ---- | ||
'''Role in Glycolysis:''' | ==='''Role in Glycolysis:'''=== | ||
====The Steps:==== | |||
:In two coupled steps, | :In two coupled steps, | ||
[[Image:GAPDH_PGK-rxn.gif|400 px]] | [[Image:GAPDH_PGK-rxn.gif|400 px]] | ||
GAPDH catalyzes the conversion of [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate glyceraldyhyde-3-phosphate] at carbon 1 to [http://en.wikipedia.org/wiki/1,3-bisphosphoglycerate 1,3-bisphosphoglycerate] (1,3-BPG). | GAPDH catalyzes the conversion of [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate glyceraldyhyde-3-phosphate] at carbon 1 to [http://en.wikipedia.org/wiki/1,3-bisphosphoglycerate 1,3-bisphosphoglycerate] (1,3-BPG). | ||
====The Reactions:==== | |||
:The reaction involving the GAPDH enzyme combines phosphorylation with oxidation in an overall [http://en.wikipedia.org/wiki/Endergonic endergonic] reaction. (ΔG°'=+6.3 kJ/mol (+1.5 kcal/mol)) First, the oxidation of glyceraldyhyde-3-phosphate to D-glycerate 1,3-bisphosphate takes place, in which an aldehyde is converted to carboxylic acid ((ΔG°'=-50 kJ/mol (-12 kcal/mol))and NAD+ ([http://en.wikipedia.org/wiki/Nicotinamide_Adenine_Dinucleotide Nicotinamide adenine dinucleotide]), an important co-factor and [http://en.wikipedia.org/wiki/Ligand ligand] found bound to the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene> of GAPDH, is simultaneously reduced endergonically to NADH. This oxidation reaction is required for the initiation of the second reaction because it is highly [http://en.wikipedia.org/wiki/Exergonic exergonic] and thus drives the endergonic second reaction ((ΔG°'=+50 kJ/mol (+12 kcal/mol)). In the second reaction a molecule of inorganic phosphate is transferred to a GAP intermediate to form a product with a high potential to transfer phosphates, 1,3-bisphosphoglycerate. | :The reaction involving the GAPDH enzyme combines phosphorylation with oxidation in an overall [http://en.wikipedia.org/wiki/Endergonic endergonic] reaction. (ΔG°'=+6.3 kJ/mol (+1.5 kcal/mol)) First, the oxidation of glyceraldyhyde-3-phosphate to D-glycerate 1,3-bisphosphate takes place, in which an aldehyde is converted to carboxylic acid ((ΔG°'=-50 kJ/mol (-12 kcal/mol))and NAD+ ([http://en.wikipedia.org/wiki/Nicotinamide_Adenine_Dinucleotide Nicotinamide adenine dinucleotide]), an important co-factor and [http://en.wikipedia.org/wiki/Ligand ligand] found bound to the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene> of GAPDH, is simultaneously reduced endergonically to NADH. This oxidation reaction is required for the initiation of the second reaction because it is highly [http://en.wikipedia.org/wiki/Exergonic exergonic] and thus drives the endergonic second reaction ((ΔG°'=+50 kJ/mol (+12 kcal/mol)). In the second reaction a molecule of inorganic phosphate is transferred to a GAP intermediate to form a product with a high potential to transfer phosphates, 1,3-bisphosphoglycerate. | ||
====The Mechanism:==== | |||
:The mechanism of GAPDH is mainly dependent the [http://en.wikipedia.org/wiki/Thiol thiol] functional group on a cysteine residue which lies within the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene>. This important thiol group acts as a [http://en.wikipedia.org/wiki/Ncleophile nucleophile], attacking the carbon on the aldehyde functional group of the [http://en.wikipedia.org/wiki/Substrate substrate], glyceraldehyde 3-phosphate, after it binds to GAPDH. The creation of a [http://en.wikipedia.org/wiki/Thiohemiacetal thiohemiacetal] intermediate occurs from this oxidative reaction, which then loses a hydride to NAD+, which is also bound nearby, forming NADH and a carboxyl group from the [http://en.wikipedia.org/wiki/Aldehyde aldehyde]. Conservation of energy is maintained through this thioester linkage to the active site cysteine. The GAP intermediate is then used in the second step, where it is important to notice that without GAPDH's use of covalent catalysis, the energy barrier of the reaction would be too high and the reaction would be too slow for living organisms. | :The mechanism of GAPDH is mainly dependent the [http://en.wikipedia.org/wiki/Thiol thiol] functional group on a cysteine residue which lies within the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene>. This important thiol group acts as a [http://en.wikipedia.org/wiki/Ncleophile nucleophile], attacking the carbon on the aldehyde functional group of the [http://en.wikipedia.org/wiki/Substrate substrate], glyceraldehyde 3-phosphate, after it binds to GAPDH. The creation of a [http://en.wikipedia.org/wiki/Thiohemiacetal thiohemiacetal] intermediate occurs from this oxidative reaction, which then loses a hydride to NAD+, which is also bound nearby, forming NADH and a carboxyl group from the [http://en.wikipedia.org/wiki/Aldehyde aldehyde]. Conservation of energy is maintained through this thioester linkage to the active site cysteine. The GAP intermediate is then used in the second step, where it is important to notice that without GAPDH's use of covalent catalysis, the energy barrier of the reaction would be too high and the reaction would be too slow for living organisms. | ||
---- | ---- | ||
'''Other roles:''' | ==='''Other roles:'''=== | ||
*The importance of GAPDH in transcription was discovered by Zheng ''et. al''. in 2003. It was found that OCA's transcriptional coactivator complex contains GAPDH, which moves between the cytosol and nucleus and may link the metabolic state to gene transcription. | *The importance of GAPDH in transcription was discovered by Zheng ''et. al''. in 2003. It was found that OCA's transcriptional coactivator complex contains GAPDH, which moves between the cytosol and nucleus and may link the metabolic state to gene transcription. | ||
*In 2005 the initiation of apoptosis was shown to be mediated by GAPDH by Hara ''et. al.'' when it was found to bind to DNA like it does in transcription activation. | *In 2005 the initiation of apoptosis was shown to be mediated by GAPDH by Hara ''et. al.'' when it was found to bind to DNA like it does in transcription activation. | ||
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*It was also found that GAPDH is plays a role in certain neruodegenerative disorders, as is able to find stretches which are encoded by the gene's CAG repeats and bind to the gene products formed from disorders such as [http://en.wikipedia.org/wiki/Huntington's_disease Huntington's disease], [http://en.wikipedia.org/wiki/Alzheimer's_disease Alzheimer’s disease], [http://en.wikipedia.org/wiki/Parkinson's_disease Parkinson’s disease] and [http://en.wikipedia.org/wiki/Machado-Joseph_disease Machado-Joseph disease]. | *It was also found that GAPDH is plays a role in certain neruodegenerative disorders, as is able to find stretches which are encoded by the gene's CAG repeats and bind to the gene products formed from disorders such as [http://en.wikipedia.org/wiki/Huntington's_disease Huntington's disease], [http://en.wikipedia.org/wiki/Alzheimer's_disease Alzheimer’s disease], [http://en.wikipedia.org/wiki/Parkinson's_disease Parkinson’s disease] and [http://en.wikipedia.org/wiki/Machado-Joseph_disease Machado-Joseph disease]. | ||
---- | ---- | ||
'''Use in the lab:''' | ==='''Use in the lab:'''=== | ||
*Overall, GAPDH is a “housekeeping gene” and is found in high levels in tissues and cells so it is commonly used in biological research as a loading control in [http://en.wikipedia.org/wiki/Western_Blot western blot] and [http://en.wikipedia.org/wiki/RT-PCR RT-PCR], but it has to be carefully controlled because under specific conditions it can have various regulation. | *Overall, GAPDH is a “housekeeping gene” and is found in high levels in tissues and cells so it is commonly used in biological research as a loading control in [http://en.wikipedia.org/wiki/Western_Blot western blot] and [http://en.wikipedia.org/wiki/RT-PCR RT-PCR], but it has to be carefully controlled because under specific conditions it can have various regulation. | ||
[[Image:GAPDH western blot.jpg|350 px]] | [[Image:GAPDH western blot.jpg|350 px]] | ||
Revision as of 04:19, 3 May 2012
| This Sandbox is Reserved from 13/03/2012, through 01/06/2012 for use in the course "Proteins and Molecular Mechanisms" taught by Robert B. Rose at the North Carolina State University, Raleigh, NC USA. This reservation includes Sandbox Reserved 451 through Sandbox Reserved 500. | ||||||
To get started:
More help: Help:Editing For more help, look at this link: http://www.proteopedia.org/wiki/index.php/Help:Getting_Started_in_Proteopedia Introduction
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StructureStructure
GAPDH has two domains, a GAPDH-like, C-terminal domain, and an NAD Binding Domain.
- The NAD (Nucleotide) Binding Domain is an Alpha Beta 3-Layer(α-β-α) Sandwich, including amino acids 1-138 and 301-340 on chains O and Q . Its CATH reports a Rossmann fold and a classification as an oxidoreductase.
- The GAPDH-like, C-terminal domain (Catalytic domain) is an Alpha Beta 2-Layer(α-β) Sandwich, including amino acids 139 - 300 on chains O and Q . Its CATH reports a holo-D-Glyceraldehyde-3-Phosphate Dehydrogenase, (domain 2) and a classification as an oxidoreductase (aldehyde(D)-NAD(A)).
ImportanceImportance
Role in Glycolysis:Role in Glycolysis:
The Steps:The Steps:
- In two coupled steps,
GAPDH catalyzes the conversion of glyceraldyhyde-3-phosphate at carbon 1 to 1,3-bisphosphoglycerate (1,3-BPG).
The Reactions:The Reactions:
- The reaction involving the GAPDH enzyme combines phosphorylation with oxidation in an overall endergonic reaction. (ΔG°'=+6.3 kJ/mol (+1.5 kcal/mol)) First, the oxidation of glyceraldyhyde-3-phosphate to D-glycerate 1,3-bisphosphate takes place, in which an aldehyde is converted to carboxylic acid ((ΔG°'=-50 kJ/mol (-12 kcal/mol))and NAD+ (Nicotinamide adenine dinucleotide), an important co-factor and ligand found bound to the of GAPDH, is simultaneously reduced endergonically to NADH. This oxidation reaction is required for the initiation of the second reaction because it is highly exergonic and thus drives the endergonic second reaction ((ΔG°'=+50 kJ/mol (+12 kcal/mol)). In the second reaction a molecule of inorganic phosphate is transferred to a GAP intermediate to form a product with a high potential to transfer phosphates, 1,3-bisphosphoglycerate.
The Mechanism:The Mechanism:
- The mechanism of GAPDH is mainly dependent the thiol functional group on a cysteine residue which lies within the . This important thiol group acts as a nucleophile, attacking the carbon on the aldehyde functional group of the substrate, glyceraldehyde 3-phosphate, after it binds to GAPDH. The creation of a thiohemiacetal intermediate occurs from this oxidative reaction, which then loses a hydride to NAD+, which is also bound nearby, forming NADH and a carboxyl group from the aldehyde. Conservation of energy is maintained through this thioester linkage to the active site cysteine. The GAP intermediate is then used in the second step, where it is important to notice that without GAPDH's use of covalent catalysis, the energy barrier of the reaction would be too high and the reaction would be too slow for living organisms.
Other roles:Other roles:
- The importance of GAPDH in transcription was discovered by Zheng et. al. in 2003. It was found that OCA's transcriptional coactivator complex contains GAPDH, which moves between the cytosol and nucleus and may link the metabolic state to gene transcription.
- In 2005 the initiation of apoptosis was shown to be mediated by GAPDH by Hara et. al. when it was found to bind to DNA like it does in transcription activation.
GAPDH was also found to be involved in ER to Golgi transport because it is recruited by rab2 to vesicular-tubular clusters of the endoplasmic reticulum where it helps form COP 1 vesicles.
- It was also found that GAPDH is plays a role in certain neruodegenerative disorders, as is able to find stretches which are encoded by the gene's CAG repeats and bind to the gene products formed from disorders such as Huntington's disease, Alzheimer’s disease, Parkinson’s disease and Machado-Joseph disease.
Use in the lab:Use in the lab:
- Overall, GAPDH is a “housekeeping gene” and is found in high levels in tissues and cells so it is commonly used in biological research as a loading control in western blot and RT-PCR, but it has to be carefully controlled because under specific conditions it can have various regulation.
ReferencesReferences
- ↑"GAPDH glyceraldehyde-3-phosphate dehydrogenase [Homo sapiens] - Gene - NCBI." National Center for Biotechnology Information. N.p., n.d. Web. 1 May 2012. Cite error: Closing
</ref>missing for<ref>tag - ↑"Glyceraldehyde 3-phosphate dehydrogenase (EC 1." European Bioinformatics Institute | Homepage | EBI. N.p., n.d. Web. 1 May 2012. [1]
- ↑"Glyceraldehyde 3-phosphate dehydrogenase - Wikipedia, the free encyclopedia." Wikipedia, the free encyclopedia. N.p., n.d. Web. 1 May 2012. [2]
- ↑"Glyceraldehyde-3-phosphate Dehydrogenase." Biochemistry Dictionary. N.p., n.d. Web. 1 May 2012. [3]
- ↑Isupov, M.N., and J.A. Littlechild. "Glyceraldehyde-3-phosphate Dehydrogenase." RCSB Protein Data Bank. N.p., 8 Oct. 1999. Web. 29 Apr. 2012. [4]
- ↑Minter, Melissa. "Glyceraldehyde-3-phosphate Dehydrogenase." Oxidoreductases and the Reactions they Catalyze. N.p., n.d. Web. 20 Apr. 2012. [5]
- ↑"Structure, Function, and Thermostability of GAPDH." GAPDH. N.p., n.d. Web. 28 Apr. 2012. [6]
- ↑Watson, H.C., and J.C. Campbell. "Twinning In Crystals Of Human Skeletal Muscle D-Glyceraldehyde-3-Phosphate Dehydrogenase." RCSB Protein Data Bank. N.p., 27 Oct. 1983. Web. 28 Apr. 2012. [7]