WordNet

a salt of phosphoric acid (同)orthophosphate, inorganic_phosphate
carbonated drink with fruit syrup and a little phosphoric acid
a sweet crystalline aldehyde formed by the breakdown of sugars (同)glyceric aldehyde

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〈U〉リン酸塩 / 《複数形で》リン酸肥料

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/08/22 21:06:58」(JST)

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Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain

crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pyrococcus horikoshii ot3

Identifiers

Symbol

Gp_dh_C

Pfam

PF02800

Pfam clan

CL0139

InterPro

IPR020829

PROSITE

PDOC00069

SCOP

1gd1

SUPERFAMILY

1gd1

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Glyceraldehyde 3-phosphate dehydrogenase (abbreviated as GAPDH or less commonly as G3PDH) (EC 1.2.1.12) is an enzyme of ~37kDa that catalyzes the sixth step of glycolysis and thus serves to break down glucose for energy and carbon molecules. In addition to this long established metabolic function, GAPDH has recently been implicated in several non-metabolic processes, including transcription activation, initiation of apoptosis,^[1] ER to Golgi vesicle shuttling, and fast axonal, or axoplasmic transport.^[2] In sperm, a testis-specific isoenzyme GAPDHS takes its role.

1 Metabolic function
- 1.1 Overall reaction catalyzed
- 1.2 Two-step conversion of glyceraldehyde-3-phosphate
- 1.3 Mechanism of catalysis
- 1.4 Enzyme regulation
- 1.5 Interactive pathway map
2 Additional functions
- 2.1 Transcription and apoptosis
3 Metabolic switch
- 3.1 ER to Golgi transport
4 Cellular location
5 Usage of GAPDH as loading control
6 References
7 Further reading

Metabolic function

As its name indicates, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyses the conversion of glyceraldehyde 3-phosphate to D-glycerate 1,3-bisphosphate. This is the 6th step in the glycolytic breakdown of glucose, an important pathway of energy and carbon molecule supply which takes place in the cytosol of eukaryotic cells. The conversion occurs in two coupled steps. The first is favourable and allows the second unfavourable step to occur.

Overall reaction catalyzed

glyceraldehyde 3-phosphate	glyceraldehyde phosphate dehydrogenase		D-glycerate 1,3-bisphosphate

	NAD⁺ +P_i	NADH + H⁺

	NAD⁺ +P_i	NADH + H⁺

Compound C00118 at KEGG Pathway Database. Enzyme 1.2.1.12 at KEGG Pathway Database. Reaction R01063 at KEGG Pathway Database. Compound C00236 at KEGG Pathway Database.

Two-step conversion of glyceraldehyde-3-phosphate

The first reaction is the oxidation of glyceraldehyde 3-phosphate at the carbon 1 position (in the diagram it is shown as the 4th carbon from glycolysis), in which an aldehyde is converted into a carboxylic acid (ΔG°'=-50 kJ/mol (-12kcal/mol)) and NAD+ is simultaneously reduced endergonically to NADH.

The energy released by this highly exergonic oxidation reaction drives the endergonic second reaction (ΔG°'=+50 kJ/mol (+12kcal/mol)), in which a molecule of inorganic phosphate is transferred to the GAP intermediate to form a product with high phosphoryl-transfer potential: 1,3-bisphosphoglycerate (1,3-BPG).

This is an example of phosphorylation coupled to oxidation, and the overall reaction is somewhat endergonic (ΔG°'=+6.3 kJ/mol (+1.5)). Energy coupling here is made possible by GAPDH.

Mechanism of catalysis

GAPDH uses covalent catalysis and general base catalysis to decrease the very large and positive activation energy of the second step of this reaction. First, a cysteine residue in the active site of GAPDH attacks the carbonyl group of GAP, creating a hemithioacetal intermediate (covalent catalysis). Next, an adjacent, tightly bound molecule of NAD⁺ accepts a hydride ion from GAP, forming NADH; GAP is concomitantly oxidized to a thioester intermediate using a molecule of water. This thioester species is much higher in energy than the carboxylic acid species that would result in the absence of GAPDH (the carboxylic acid species is so low in energy that the energy barrier for the second step of the reaction (phosphorylation) would be too high, and the reaction, therefore, too slow and equilibrium too unfavorable for a living organism). Donation of the hydride ion by the hemithioacetal is facilitated by its deprotonation by a histidine residue in the enzyme's active site (general base catalysis). Deprotonation encourages the reformation of the carbonyl group in the thioester intermediate and ejection of the hydride ion. NADH leaves the active site and is replaced by another molecule of NAD⁺, the positive charge of which stabilizes the negatively charged carbonyl oxygen in the transition state of the next and ultimate step. Finally, a molecule of inorganic phosphate attacks the thioester and forms a tetrahedral intermediate, which then collapses to release 1,3-bisphosphoglycerate, and the thiol group of the enzyme's cysteine residue.

Enzyme regulation

This protein may use the morpheein model of allosteric regulation.^[3]

Interactive pathway map

Click on genes, proteins and metabolites below to link to respective articles. ^{[§ 1]}

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|{{{bSize}}}px|alt=Glycolysis and Gluconeogenesis edit]]

File:WP534.png

Glycolysis and Gluconeogenesis edit

^ The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534".

Additional functions

GAPDH, like many other enzymes, has multiple functions. In addition to catalysing the 6th step of glycolysis, recent evidence implicates GAPDH in other cellular processes.GAPDH has been described to exhibit higher order multifunctionality in the context of maintaining cellular iron homeostasis.^[4] This came as a surprise to researchers but it makes evolutionary sense to re-use and adapt existing proteins instead of evolving a novel protein from scratch.

GAPDH can also be inhibited by arsenate, inhibiting glycolysis in red blood cells and causing hemolytic anemia.

Transcription and apoptosis

GAPDH can itself activate transcription. The OCA-S transcriptional coactivator complex contains GAPDH and lactate dehydrogenase, two proteins previously only thought to be involved in metabolism. GAPDH moves between the cytosol and the nucleus and may thus link the metabolic state to gene transcription.^[5]

In 2005, Hara et al. showed that GAPDH initiates apoptosis. This is not a third function, but can be seen as an activity mediated by GAPDH binding to DNA like in transcription activation, discussed above. The study demonstrated that GAPDH is S-nitrosylated by NO in response to cell stress, which causes it to bind to the protein SIAH1, a ubiquitin ligase. The complex moves into the nucleus where Siah1 targets nuclear proteins for degradation, thus initiating controlled cell shutdown.^[6] In subsequent study the group demonstrated that deprenyl, which has been used clinically to treat Parkinson's disease, strongly reduces the apoptotic action of GAPDH by preventing its S-nitrosylation and might thus be used as a drug.^[7]

Metabolic switch

GAPDH acts as reversible metabolic switch under oxidative stress.^[8] When cells are exposed to oxidants, they need excessive amounts of the antioxidant cofactor NADPH. In the cytosol, NADPH is reduced from NADP+ by several enzymes, three of them catalyze the first steps of the Pentose phosphate pathway. Oxidant-treatments cause an inactivation of GAPDH. This inactivation re-routes temporally the metabolic flux from glycolysis to the Pentose Phosphate Pathway, allowing the cell to generate more NADPH.^[9] Under stress conditions, NADPH is needed by some antioxidant-systems including glutaredoxin and thioredoxin as well as being essential for the recycling of gluthathione.

ER to Golgi transport

GAPDH also appears to be involved in the vesicle transport from the endoplasmic reticulum (ER) to the Golgi apparatus which is part of shipping route for secreted proteins. It was found that GAPDH is recruited by rab2 to the vesicular-tubular clusters of the ER where it helps to form COP 1 vesicles. GAPDH is activated via tyrosine phosphorylation by Src.^[10]

Cellular location

All steps of glycolysis take place in the cytosol and so does the reaction catalysed by GAPDH. Research in red blood cells indicates that GAPDH and several other glycolytic enzymes assemble in complexes on the inside of the cell membrane. The process appears to be regulated by phosphorylation and oxygenation.^[11] Bringing several glycolytic enzymes close to each other is expected to greatly increase the overall speed of glucose breakdown. Recent studies have also revealed that GAPDH is expressed in an iron dependent fashion on the exterior of the cell membrane a where it plays a role in maintenance of cellular iron homeostasis.^[12]^[13]

Usage of GAPDH as loading control

Because the GAPDH gene is often stably and constitutively expressed at high levels in most tissues and cells, it is considered a housekeeping gene. For this reason, GAPDH is commonly used by biological researchers as a loading control for western blot and as a control for qPCR. However, researchers have reported different regulation of GAPDH under specific conditions.^[14] For example, the transcription factor MZF-1 has been shown to regulate the GAPDH gene.^[15] Therefore, the use of GAPDH as loading control has to be considered carefully.

References

^ Tarze A, Deniaud A, Le Bras M, Maillier E, Molle D, Larochette N, Zamzami N, Jan G, Kroemer G, Brenner C (Apr 2007). "GAPDH, a novel regulator of the pro-apoptotic mitochondrial membrane permeabilization". Oncogene 26 (18): 2606–20. doi:10.1038/sj.onc.1210074. PMID 17072346.
^ Zala D, Hinckelmann MV, Yu H, Lyra da Cunha MM, Liot G, Cordelières FP, Marco S, Saudou F (Jan 2013). "Vesicular glycolysis provides on-board energy for fast axonal transport". Cell 152 (3): 479–91. doi:10.1016/j.cell.2012.12.029. PMID 23374344.
^ Selwood T, Jaffe EK (Mar 2012). "Dynamic dissociating homo-oligomers and the control of protein function". Archives of Biochemistry and Biophysics 519 (2): 131–43. doi:10.1016/j.abb.2011.11.020. PMC 3298769. PMID 22182754.
^ Boradia VM, Raje M, Raje CI (Dec 2014). "Protein moonlighting in iron metabolism: glyceraldehyde-3-phosphate dehydrogenase (GAPDH)". Biochemical Society Transactions 42 (6): 1796–801. doi:10.1042/BST20140220. PMID 25399609.
^ Zheng L, Roeder RG, Luo Y (Jul 2003). "S phase activation of the histone H2B promoter by OCA-S, a coactivator complex that contains GAPDH as a key component". Cell 114 (2): 255–66. doi:10.1016/S0092-8674(03)00552-X. PMID 12887926.
^ Hara MR, Agrawal N, Kim SF, Cascio MB, Fujimuro M, Ozeki Y, Takahashi M, Cheah JH, Tankou SK, Hester LD, Ferris CD, Hayward SD, Snyder SH, Sawa A (Jul 2005). "S-nitrosylated GAPDH initiates apoptotic cell death by nuclear translocation following Siah1 binding". Nature Cell Biology 7 (7): 665–74. doi:10.1038/ncb1268. PMID 15951807.
^ Hara MR, Thomas B, Cascio MB, Bae BI, Hester LD, Dawson VL, Dawson TM, Sawa A, Snyder SH (Mar 2006). "Neuroprotection by pharmacologic blockade of the GAPDH death cascade". Proceedings of the National Academy of Sciences of the United States of America 103 (10): 3887–9. doi:10.1073/pnas.0511321103. PMC 1450161. PMID 16505364.
^ Agarwal AR, Zhao L, Sancheti H, Sundar IK, Rahman I, Cadenas E (Nov 2012). "Short-term cigarette smoke exposure induces reversible changes in energy metabolism and cellular redox status independent of inflammatory responses in mouse lungs". American Journal of Physiology. Lung Cellular and Molecular Physiology 303 (10): L889–98. doi:10.1152/ajplung. PMID 23064950.
^ Ralser M, Wamelink MM, Kowald A, Gerisch B, Heeren G, Struys EA, Klipp E, Jakobs C, Breitenbach M, Lehrach H, Krobitsch S (2007). "Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress". Journal of Biology 6 (4): 10. doi:10.1186/jbiol61. PMC 2373902. PMID 18154684.
^ Tisdale EJ, Artalejo CR (Jun 2007). "A GAPDH mutant defective in Src-dependent tyrosine phosphorylation impedes Rab2-mediated events". Traffic 8 (6): 733–41. doi:10.1111/j.1600-0854.2007.00569.x. PMID 17488287.
^ Campanella ME, Chu H, Low PS (Feb 2005). "Assembly and regulation of a glycolytic enzyme complex on the human erythrocyte membrane". Proceedings of the National Academy of Sciences of the United States of America 102 (7): 2402–7. doi:10.1073/pnas.0409741102. PMC 549020. PMID 15701694.
^ Sirover MA (Dec 2014). "Structural analysis of glyceraldehyde-3-phosphate dehydrogenase functional diversity". The International Journal of Biochemistry & Cell Biology 57: 20–6. doi:10.1016/j.biocel.2014.09.026. PMID 25286305.
^ Kumar S, Sheokand N, Mhadeshwar MA, Raje CI, Raje M (Jan 2012). "Characterization of glyceraldehyde-3-phosphate dehydrogenase as a novel transferrin receptor". The International Journal of Biochemistry & Cell Biology 44 (1): 189–99. doi:10.1016/j.biocel.2011.10.016. PMID 22062951.
^ Barber RD, Harmer DW, Coleman RA, Clark BJ (May 2005). "GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues". Physiological Genomics 21 (3): 389–95. doi:10.1152/physiolgenomics.00025.2005. PMID 15769908.
^ Piszczatowski RT, Rafferty BJ, Rozado A, Tobak S, Lents NH (Aug 2014). "The glyceraldehyde 3-phosphate dehydrogenase gene (GAPDH) is regulated by myeloid zinc finger 1 (MZF-1) and is induced by calcitriol". Biochemical and Biophysical Research Communications 451 (1): 137–41. doi:10.1016/j.bbrc.2014.07.082. PMID 25065746.

UpToDate Contents

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1. グルコース-6-リン酸脱水素酵素欠損症の診断および治療 diagnosis and treatment of glucose 6 phosphate dehydrogenase deficiency
2. グルコース-6-リン酸脱水素酵素欠損症の臨床症状 clinical manifestations of glucose 6 phosphate dehydrogenase deficiency
3. グルコース-6-リン酸脱水素酵素欠損症の遺伝学および病態生理 genetics and pathophysiology of glucose 6 phosphate dehydrogenase deficiency
4. 小児における溶血性貧血の概要 overview of hemolytic anemias in children
5. ヘキソースリン酸側路およびグルタチオン代謝疾患（グルコース-6-リン酸脱水素酵素欠損症を除く） disorders of the hexose monophosphate shunt and glutathione metabolism other than glucose 6 phosphate dehydrogenase deficiency

English Journal

Small changes huge impact: the role of thioredoxin 1 in the regulation of apoptosis by S-nitrosylation.

Li H, Wan A, Xu G, Ye D.SourceSchool of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
Acta biochimica et biophysica Sinica.Acta Biochim Biophys Sin (Shanghai).2013 Mar;45(3):153-61. doi: 10.1093/abbs/gms103. Epub 2012 Dec 4.
Nitric oxide (NO) is a bioregulator of apoptosis, which has both antiapoptotic and proapoptotic functions. However, the molecular mechanisms responsible for its opposite biological effects are not fully understood. Recent advances in the study of protein S-nitrosylation may provide novel insights in
PMID 23212077
PMID 23124112

Japanese Journal

尿中剥離細胞 survivin mRNA 測定による膀胱癌の診断

坂本佑子,西岡淳二,野間桂,安田和成,中谷中,木瀬英明,杉村芳樹,登勉
臨床病理 59(5), 446-451, 2011-05-25
NAID 10029427344

★リンクテーブル★

リンク元	「解糖系」「グリセルアルデヒド-3-リン酸脱水素酵素」「グリセルアルデヒド3リン酸デヒドロゲナーゼ」「G3PD」「GAPD」
拡張検索	「NAD-dependent glyceraldehyde-3-phosphate dehydrogenase」「chloroplast glyceraldehyde-3-phosphate dehydrogenase」
関連記事	「phosphate」「glyceraldehyde」「dehydrogenase」「dehydrogenases」

「解糖系」

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
	determinants of enzyme thermostability observed in the molecular structure of thermus aquaticus d-glyceraldehyde-3-phosphate dehydrogenase at 2.5 angstroms resolution
Identifiers
Symbol	Gp_dh_N
Pfam	PF00044
Pfam clan	CL0063
InterPro	IPR020828
PROSITE	PDOC00069
SCOP	1gd1
SUPERFAMILY	1gd1
Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Glyceraldehyde-3-phosphate dehydrogenase
	GAPDH with NAD+ and Pi bound to the active site. PDB rendering based on 2CZC.
Available structures
PDB	Ortholog search: PDBe, RCSB
List of PDB id codes
	1U8F, 1ZNQ, 2FEH, 3GPD, 4WNC, 4WNI
Identifiers
Symbols	GAPDH ; G3PD; GAPD; HEL-S-162eP
External IDs	OMIM: 138400 MGI: 3646088 HomoloGene: 107053 ChEMBL: 2284 GeneCards: GAPDH Gene
EC number	1.2.1.12
Gene ontology
Molecular function	• glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity; • protein binding; • microtubule binding; • peptidyl-cysteine S-nitrosylase activity; • identical protein binding; • NADP binding; • NAD binding;
Cellular component	• nucleus; • cytoplasm; • lipid particle; • cytosol; • plasma membrane; • microtubule cytoskeleton; • membrane; • ribonucleoprotein complex; • nuclear membrane; • vesicle; • intracellular membrane-bounded organelle; • perinuclear region of cytoplasm; • extracellular exosome; • GAIT complex;
Biological process	• microtubule cytoskeleton organization; • carbohydrate metabolic process; • glucose metabolic process; • gluconeogenesis; • negative regulation of translation; • peptidyl-cysteine S-trans-nitrosylation; • small molecule metabolic process; • protein stabilization; • neuron apoptotic process; • oxidation-reduction process; • canonical glycolysis; • cellular response to interferon-gamma;
	Sources: Amigo / QuickGO
RNA expression pattern
	More reference expression data
Orthologs
	v; t; e;

　　[★]

英: glycolytic pathway
同: エムデン-マイヤーホフ経路 Embden-Meyerhof pathway
関: 解糖、TCA回路

CH(OH)-CH(OH)-C(OH)H-CH(OH)-C(CH2OH)H-O- グルコース (OHが↓↓↑↓↑)
CH(OH)-CH(OH)-C(OH)H-CH(OH)-C(CH2O-PO3)H-O- グルコース-6-リン酸 (OHが↓↓↑↓↑)
C(CH2OH)OH-C(OH)H-CH(OH)-C(CH2O-PO3)H-O- フルクトース-6-リン酸
C(CH2O-PO3)OH-C(OH)H-CH(OH)-C(CH2O-PO3)H-O- フルクトース-1,6-リン酸

glucose
↓-hexokinase/glucokinase(liver)
glucose 6-phosphate
↓-phosphohexose isomerase
fructose 6-phosphate
↓-phosphofructokinase
fructose 1,6-bisphosphate
↓-aldolase
glyceraldehyde 3-phosphate
↓-glyceraldehyde-3-phosphate dehydrogenase
1,3-bisphosphoglycerate
↓-phosphoglycerate kinase →ATP
3-phosphoglycerate
↓-phosphoglyceate mutase
2-phosphoglycerate
↓-enolase
phosphoenolpyruvate
↓-pyruvate kinase → ATP
pyruvate
　－(pyruvate dehydrogenase)→acetyl-CoA
　－(pyruvate carboxylase)→oxaloacetate－(NADH+H+)→malate

解糖系の酵素 (first aid step1 2006 p.87, FASTEP1_87_酵素一覧.xls)

1	galactokinase	キナーゼ
2	galactose-1-phosphate uridyltransferase	転移酵素
3	hexokinase/glucokinase	キナーゼ
4	glucose-6-phosphatase	ホスファターゼ
5	glucose-6-phosphate dehydrogenase	脱水素酵素
6	transketolase
7	phosphofructokinase	キナーゼ
8	fructose-1,6-bisphosphatase	ホスファターゼ
9	fructokinase	キナーゼ	フルクトキナーゼ
10	aldolase B		アルドラーゼ
11	pyruvate kinase	キナーゼ	ピルビン酸キナーゼ
12	pyruvate dehydrogenase	脱水素酵素	ピルビン酸デヒドロゲナーゼ
13	HMG-CoA reductase	還元酵素	HMG-CoA還元酵素
14	pyruvate carboxylase	カルボキシラーゼ	ピルビン酸カルボキシラーゼ
15	PEP carboxykinase	キナーゼ	PEPカルボキシキナーゼ
16	citrate synthase	合成酵素	クエン酸合成酵素
17	α-ketoglutarate dehydrogenase	脱水素酵素	α-ケトグルタミン酸脱水素酵素
18	ornithine transcarbamylase	転移酵素	オルニチンカルバモイルトランスフェラーゼ