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158  structures 5613  species 2  interactions 10194  sequences 13  architectures

Family: Gp_dh_N (PF00044)

Summary: Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Glyceraldehyde 3-phosphate dehydrogenase". More...

Glyceraldehyde 3-phosphate dehydrogenase Edit Wikipedia article

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
Identifiers
Symbols GAPDH; G3PD; GAPD
External IDs OMIM: 138400 MGI: 3646088 HomoloGene: 107053 ChEMBL: 2284 GeneCards: GAPDH Gene
EC number 1.2.1.12
RNA expression pattern
PBB GE GAPDH 212581 x at tn.png
PBB GE GAPDH 213453 x at tn.png
PBB GE GAPDH 217398 x at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 2597 100043349
Ensembl ENSG00000111640 ENSMUSG00000078370
UniProt P04406 P16858
RefSeq (mRNA) NM_001256799.1 NM_008084
RefSeq (protein) NP_001243728.1 NP_001074766
Location (UCSC) Chr 12:
6.64 – 6.65 Mb		 Chr 12:
71.02 – 71.02 Mb
PubMed search [1] [2]
This box:
Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
PDB 1cer EBI.jpg
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
Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
PDB 2czc EBI.jpg
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

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] and ER to Golgi vesicle shuttling.

Contents

[edit] 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.

[edit] Overall reaction catalyzed

glyceraldehyde 3-phosphate glyceraldehyde phosphate dehydrogenase D-glycerate 1,3-bisphosphate
D-glyceraldehyde-3-phosphate wpmp.png   222px-1,3-bisphospho-D-glycerate.svg.png
NAD+ + Pi NADH + H+
Biochem reaction arrow reversible YYYY horiz med.png
NAD+ + Pi 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.

[edit] 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.

[edit] 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.

[edit] Enzyme Regulation

This protein may use the morpheein model of allosteric regulation. [2]


[edit] 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.

[edit] 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. [3]

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. [4] 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. [5]

[edit] 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.[6] Under stress conditions, NADPH is needed by some antioxidant-systems including glutaredoxin and thioredoxin as well as being essential for the recycling of gluthathione.

[edit] 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. [7]

[edit] 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. [8] Bringing several glycolytic enzymes close to each other is expected to greatly increase the overall speed of glucose breakdown.

[edit] 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.[9] Therefore, the use of GAPDH as loading control has to be controlled carefully.

[edit] 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. PMID 17072346. 
  2. ^ T. Selwood and E. K. Jaffe. (2011). "Dynamic dissociating homo-oligomers and the control of protein function.". Arch. Biochem. Biophys. 519 (2): 131–43. doi:10.1016/j.abb.2011.11.020. PMID 22182754. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=22182754. 
  3. ^ 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. PMID 12887926. 
  4. ^ 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. PMID 15951807. 
  5. ^ Hara MR, Thomas B, Cascio MB, et al. (2006). "Neuroprotection by pharmacologic blockade of the GAPDH death cascade". Proc. Natl. Acad. Sci. U.S.A. 103 (10): 3887–9. doi:10.1073/pnas.0511321103. PMC 1450161. PMID 16505364. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1450161. 
  6. ^ Ralser M et al. (2007). "Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress.". J Biol 6 (11): 10. doi:10.1186/jbiol61. PMC 2373902. PMID 18154684. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2373902. 
  7. ^ 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. PMID 17488287. 
  8. ^ Campanella ME, Chu H, Low PS (2005). "Assembly and regulation of a glycolytic enzyme complex on the human erythrocyte membrane". Proc. Natl. Acad. Sci. U.S.A. 102 (7): 2402–7. doi:10.1073/pnas.0409741102. PMC 549020. PMID 15701694. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=549020. 
  9. ^ 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. PMID 15769908. 

[edit] Further reading

Glycolysis Metabolic Pathway
Glucose Hexokinase Glucose 6-phosphate Glucose-6-phosphate isomerase Fructose 6-phosphate phosphofructokinase-1 Fructose 1,6-bisphosphate Fructose bisphosphate aldolase
D-glucose wpmp.png ATP ADP Alpha-D-glucose-6-phosphate wpmp.png Beta-D-fructose-6-phosphate wpmp.png ATP ADP Beta-D-fructose-1,6-bisphosphate wpmp.png
Biochem reaction arrow foward YYNN horiz med.svg GG-Pfeil 1.svg Biochem reaction arrow foward YYNN horiz med.svg GG-Pfeil 1.svg
Dihydroxyacetone phosphate Glyceraldehyde 3-phosphate Triosephosphate isomerase Glyceraldehyde 3-phosphate Glyceraldehyde-3-phosphate dehydrogenase 1,3-Bisphosphoglycerate
Glycerone-phosphate wpmp.png D-glyceraldehyde-3-phosphate wpmp.png D-glyceraldehyde-3-phosphate wpmp.png NAD+ + Pi NADH + H+ 1,3-bisphospho-D-glycerate.svg
+ GG-Pfeil 1.svg 2 Biochem reaction arrow reversible YYYY horiz med.svg 2
Phosphoglycerate kinase 3-Phosphoglycerate Phosphoglycerate mutase 2-Phosphoglycerate Phosphopyruvate hydratase(Enolase) Phosphoenolpyruvate Pyruvate kinase Pyruvate
ADP ATP 3-phospho-D-glycerate.svg 2-phospho-D-glycerate wpmp.png H2O Phosphoenolpyruvate wpmp.png ADP ATP Pyruvic-acid-2D-skeletal.svg
Biochem reaction arrow reversible YYYY horiz med.svg 2 GG-Pfeil 1.svg 2 Biochem reaction arrow reversible NYYN horiz med.png 2 Biochem reaction arrow foward YYNN horiz med.svg 2

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m(A16/C10),i(k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)
Glycolysis
Gluconeogenesis only
Regulatory

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m(A16/C10),i(k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)
Aldehyde/oxo oxidoreductases (EC 1.2)
1.2.1: NAD or NADP
1.2.2: cytochrome
1.2.3: oxygen
1.2.4: disulfide
1.2.7: iron-sulfur protein

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Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain

GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold.

Literature references

  1. Kim H, Feil IK, Verlinde CL, Petra PH, Hol WG; , Biochemistry 1995;34:14975-14986.: Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Leishmania mexicana: implications for structure-based drug design and a new position for the inorganic phosphate binding site. PUBMED:7578111

Clan

This family is a member of clan NADP_Rossmann (CL0063), which has a total of 178 members.

External database links

HOMSTRAD: gpdh
PANDIT: PF00044
PROSITE: PDOC00069
Pseudofam: PF00044
SCOP: 1gd1
SYSTERS: Gp_dh_N

This tab holds annotation information from the InterPro database.

InterPro entry IPR020828

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis [PUBMED:2716055] by reversibly catalysing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. The enzyme exists as a tetramer of identical subunits, each containing 2 conserved functional domains: an NAD-binding domain, and a highly conserved catalytic domain [PUBMED:6303388]. The enzyme has been found to bind to actin and tropomyosin, and may thus have a role in cytoskeleton assembly. Alternatively, the cytoskeleton may provide a framework for precise positioning of the glycolytic enzymes, thus permitting efficient passage of metabolites from enzyme to enzyme [PUBMED:6303388].

GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location. For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis [PUBMED:10740219]. The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription. The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself.

GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington's disease, Alzheimer's disease, Parkinson's disease and Machado-Joseph disease through stretches encoded by their CAG repeats. Abnormal neuronal apoptosis is associated with these diseases. Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins [PUBMED:12721812].

This entry represents the N-terminal domain which is a Rossmann NAD(P) binding fold.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan NADP_Rossmann (CL0063), which contains the following 178 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa Bac_GDH Bin3 CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 DAO DapB_N DFP DNA_circ_N DNA_methylase DOT1 DREV dTMP_synthase DUF1442 DUF1776 DUF2431 DUF268 DUF3321 DUF43 DUF519 DUF633 DUF938 DXP_redisom_C DXP_reductoisom Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ G-7-MTase G6PD_N GCD14 GDI GFO_IDH_MocA GIDA GidB GLF Glyco_hydro_4 GMC_oxred_N Gp_dh_N GRDA HI0933_like HIM1 IlvN K_oxygenase KR LCM Ldh_1_N Lycopene_cycl Malic_M Mannitol_dh Met_10 Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_26 Methyltransf_27 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS Nol1_Nop2_Fmu Nol1_Nop2_Fmu_2 NSP13 OCD_Mu_crystall PARP_regulatory PCMT PDH Polysacc_synt_2 Pox_MCEL Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 Saccharop_dh SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth Strep_67kDa_ant TehB THF_DHG_CYH_C Thi4 ThiF TPMT TrkA_N TRM TRM13 tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 V_cholerae_RfbT XdhC_C YjeF_N

Alignments

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Trees

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Curation and family details

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Curation View help on the curation process

Seed source: Overington
Previous IDs: gpdh;
Type: Domain
Author: Eddy SR, Griffiths-Jones SR
Number in seed: 112
Number in full: 10194
Average length of the domain: 129.40 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 43.57 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.6
Model length: 151
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 2 interactions for this family. More...

Gp_dh_N Gp_dh_C

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Gp_dh_N domain has been found. There are 158 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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