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Glyceraldehyde 3-phosphate dehydrogenase

From Wikipedia, the free encyclopedia
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Glyceraldehyde 3-phosphate dehydrogenase (abbreviated as /w/index.php?title=Template:PBB/2597&
GAPDH or less commonly as G3PDH) (EC 1.2.1.12 action=edit)

-3-phosphate dehydrogenase

3GPD (http://www.pdbe.org/3gpd) .

vailable structures
bId=1u8f) , 1znq (http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1znq)

Identifiers

g/searches/accession_report.cgi?id=MGI:3646088) HomoloGene: 107053 (http://www.ncbi.nlm.nih.gov/entrez

http://www.genecards.org/cgi-bin/carddisp.pl?id_type=entrezgene&id=2597)

Gene Ontology
ogy.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=GO:0004365)
search_constraint=terms&depth=0&query=GO:0016491)
nstraint=terms&depth=0&query=GO:0051287)
rms&depth=0&query=GO:0005737)
s&search_constraint=terms&depth=0&query=GO:0006006)
rms&depth=0&query=GO:0006096)
gp=UniProtKB:P04406) / QuickGO (http://www.ebi.ac.uk/QuickGO/GProtein?ac=P04406)

A expression pattern

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http://biogps.gnf.org/gene/2597/)

Orthologs

Mouse
622339 (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids=622339&rn=1)

ENSMUSG00000078370 (http://www.ensembl.org/Mus_musculus/geneview?gene=ENSMUSG00000078370;db=core)

n/a

NM_008084 (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_008084)

NP_001074766 (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NP_001074766)

Chr 12:
7780) 71.02 - 71.02 Mb (http://genome.ucsc.edu/cgi-bin/hgTracks?org=Mouse&db=mm8&position=chr12:71021068-71022717)

[2] (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid=622339)

(http://www.expasy.org/cgi-bin/nicezyme.pl?1.2.1.12) ) is an enzyme 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] and ER to Golgi vesicle shuttling.

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Contents
1 Metabolic function
1.1 Overall reaction catalyzed
1.2 Two-step conversion of glyceraldehyde-3-phosphate
1.3 Mechanism of catalysis
2 Additional functions
2.1 Transcription and apoptosis
3 Metabolic Switch
3.1 ER to Golgi transport
4 Cellular location
5 Miscellaneous
5.1 References
6 Further reading

Metabolic function
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyses the conversion of glyceraldehyde 3-phosphate
as the name indicates. This is the 6th step of the breakdown of glucose (glycolysis), an important pathway of
energy and carbon molecule supply located in the cytosol of eukaryotic cells. Glyceraldehyde 3-phosphate is
converted to D-glycerate 1,3-bisphosphate in two coupled steps. The first is favourable and allows the second
unfavourable step to occur.

Overall reaction catalyzed

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

NAD+ NADH
+ P i + H+

NAD+ NADH
+ P i + H+

Compound C00118 (http://www.genome.jp/dbget-bin/www_bget?compound+C00118) at KEGG Pathway Database. Enzyme 1.2.1.12 (http://www.genome.jp/dbget-

bin/www_bget?enzyme+1.2.1.12) at KEGG Pathway Database. Reaction R01063 (http://www.genome.jp/dbget-bin/www_bget?rn+R01063) at KEGG Pathway Database. Compound
C00236 (http://www.genome.jp/dbget-bin/www_bget?compound+C00236) at KEGG Pathway Database.

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Two-step conversion of glyceraldehyde-3-phosphate

The first reaction is the oxidation of glyceraldehyde 3-phosphate at the carbon 1 position (the 4th carbon from
glycolysis which is shown in the diagram), 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 great, and the
reaction therefore too slow, 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.

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. 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.

Transcription and apoptosis

Zheng et al. discovered in 2003 that 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. [2]

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. [3] 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. [4]

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Metabolic Switch
GAPDH acts as reversible metabolic switch under oxidative stress. 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.[5] 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. [6]

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. [7] Bringing
several glycolytic enzymes close to each other is expected to greatly increase the overall speed of glucose
breakdown.

Miscellaneous
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 RT-PCR. However, researchers have reported different
regulation of GAPDH under specific conditions.[8] Therefore, the use of GAPDH as loading control has to be
controlled carefully.

References
1. ^ A. Tarze, A. Deniaud, M. Le Bras, E. Maillier, D. Molle, N. Larochette, N. Zamzami, G. Jan, G. Kroemer, and C.
Brenner (2007). "GAPDH, a novel regulator of the pro-apoptotic mitochondrial membrane permeabilization".
Oncogene 26 (18): 2606–2620. doi:10.1038/sj.onc.1210074 (http://dx.doi.org/10.1038%2Fsj.onc.1210074) .
PMID 17072346 (http://www.ncbi.nlm.nih.gov/pubmed/17072346) .
2. ^ Zheng L, Roeder RG, Luo Y (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
(http://dx.doi.org/10.1016%2FS0092-8674%2803%2900552-X) . PMID 12887926 (http://www.ncbi.nlm.nih.gov
/pubmed/12887926) .
3. ^ Hara MR, Agrawal N, Kim SF, et al. (2005). "S-nitrosylated GAPDH initiates apoptotic cell death by nuclear
translocation following Siah1 binding". Nat. Cell Biol. 7 (7): 665–74. doi:10.1038/ncb1268 (http://dx.doi.org
/10.1038%2Fncb1268) . PMID 15951807 (http://www.ncbi.nlm.nih.gov/pubmed/15951807) .
4. ^ Hara MR, Thomas B, Cascio MB, et al. (2006). "Neuroprotection by pharmacologic blockade of the GAPDH
death cascade" (http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1450161) . Proc. Natl.

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Acad. Sci. U.S.A. 103 (10): 3887–9. doi:10.1073/pnas.0511321103 (http://dx.doi.org

/10.1073%2Fpnas.0511321103) . PMC 1450161 (http://www.pubmedcentral.gov
/articlerender.fcgi?tool=pmcentrez&artid=1450161) . PMID 16505364 (http://www.ncbi.nlm.nih.gov/pubmed
/16505364) . http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1450161.
5. ^ Ralser M et al. (2007). "Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress."
(http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2373902) . J Biol 6 (11): 10.
doi:10.1186/jbiol61 (http://dx.doi.org/10.1186%2Fjbiol61) . PMC 2373902 (http://www.pubmedcentral.gov
/articlerender.fcgi?tool=pmcentrez&artid=2373902) . PMID 18154684 (http://www.ncbi.nlm.nih.gov/pubmed
/18154684) . http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2373902.
6. ^ Tisdale EJ, Artalejo CR (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 (http://dx.doi.org
/10.1111%2Fj.1600-0854.2007.00569.x) . PMID 17488287 (http://www.ncbi.nlm.nih.gov/pubmed/17488287) .
7. ^ Campanella ME, Chu H, Low PS (2005). "Assembly and regulation of a glycolytic enzyme complex on the human
erythrocyte membrane" (http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=549020) .
Proc. Natl. Acad. Sci. U.S.A. 102 (7): 2402–7. doi:10.1073/pnas.0409741102 (http://dx.doi.org
/10.1073%2Fpnas.0409741102) . PMC 549020 (http://www.pubmedcentral.gov/articlerender.fcgi?tool=pmcentrez&
artid=549020) . PMID 15701694 (http://www.ncbi.nlm.nih.gov/pubmed/15701694) .
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=549020.
8. ^ Robert D. Barber , Dan W. Harmer , Robert A. Coleman and Brian J. Clark (2005). "GAPDH as a housekeeping
gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues". Physiological Genomics 21 (3):
389-395. doi:10.1152/physiolgenomics.00025.2005 (http://dx.doi.org/10.%E2%80%8B1152%2F%E2
%80%8Bphysiolgenomics.%E2%80%8B00025.%E2%80%8B2005) . PMID 15769908
(http://www.ncbi.nlm.nih.gov/pubmed/15769908) .

Further reading
Voet D, Voet JG (2010). Biochemistry. New York: Wiley. ISBN 0-470-57095-4.
Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2002). Biochemistry, Fifth Edition & Lecture
Notebook. San Francisco: W. H. Freeman. ISBN 0-7167-9804-2.
diagram of the GAPDH reaction mechanism (http://www.ncbi.nlm.nih.gov/books
/bv.fcgi?highlight=glyceraldehyde+3+phosphate+dehydrogenase&rid=mcb.figgrp.4342&
WebEnv=0bpB8XePphZ8qSS3b9o1BB3FMZtXPr7yFc3MxfLR12WUi7sKapf987mBijj9A0v-
LwF_W_lLjUKNwY%40D45D6EC76612AEB0_0018SID&WebEnvRq=1) from Lodish MCB at NCBI
bookshelf
similar diagram (http://www.ncbi.nlm.nih.gov/books
/bv.fcgi?highlight=glyceraldehyde+3+phosphate+dehydrogenase&rid=mboc4.figgrp.297&
WebEnv=0qL7ctlqrxJxTMzSHUlui3y2aeU6B8K6Tblugar02bi5Eetekc7g1j_m9gRDhWr1NM3L7U4G-
5GFjf%40D45D6EC76612AEB0_0018SID&WebEnvRq=1) from Alberts The Cell at NCBI bookshelf
Retrieved from "http://en.wikipedia.org/wiki/Glyceraldehyde_3-phosphate_dehydrogenase"
Categories: Human proteins | Glycolysis | EC 1.2.1

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