Summary: NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
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Glycerol-3-phosphate dehydrogenase Edit Wikipedia article
|Glycerol-3-phosphate dehydrogenase (NAD+)|
Crystallographic structure of human glycerol-3-phosphate dehydrogenase 1.
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
|Glycerol-3-phosphate dehydrogenase (quinone)|
|PDB structures||RCSB PDB PDBe PDBsum|
|NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus|
crystal structure of the n-(1-d-carboxylethyl)-l-norvaline dehydrogenase from arthrobacter sp. strain 1c
|NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus|
structure of glycerol-3-phosphate dehydrogenase from archaeoglobus fulgidus
Glycerol-3-phosphate dehydrogenase (GPDH) is an enzyme that catalyzes the reversible redox conversion of dihydroxyacetone phosphate (a.k.a. glycerone phosphate, outdated) to sn-glycerol 3-phosphate.
Glycerol-3-phosphate dehydrogenase serves as a major link between carbohydrate metabolism and lipid metabolism. It is also a major contributor of electrons to the electron transport chain in the mitochondria.
Older terms for glycerol-3-phosphate dehydrogenase include alpha glycerol-3-phosphate dehydrogenase (alphaGPDH) and glycerolphosphate dehydrogenase (GPDH). However, glycerol-3-phosphate dehydrogenase is not the same as glyceraldehyde 3-phosphate dehydrogenase (GAPDH), whose substrate is an aldehyde not an alcohol.
GPDH plays a major role in lipid biosynthesis. Through the reduction of dihydroxyacetone phosphate into glycerol 3-phosphate, GPDH allows the prompt dephosphorylation of glycerol 3-phosphate into glycerol. Additionally, GPDH is one of the enzymes involved in maintaining the redox potential across the inner mitochondrial membrane.
The NAD+/NADH coenzyme couple act as an electron reservoir for metabolic redox reactions, carrying electrons from one reaction to another. Most of these metabolism reactions occur in the mitochondria. To regenerate NAD+ for further use, NADH pools in the cytosol must be reoxidized. Since the mitochondrial inner membrane is impermeable to both NADH and NAD+, these cannot be freely exchanged between the cytosol and mitochondrial matrix.
One way to shuttle this reducing equivalent across the membrane is through the Glycerol-3-phosphate shuttle, which employs the two forms of GPDH:
- Cytosolic GPDH, or GPD1 is located in the mitochondrial inner-membrane space or cytosol, and catalyzes the reduction of dihydroxyacetone phosphate into glycerol-3-phosphate.
- In conjunction, Mitochondrial GPDH, or GPD2 is embedded on the outer surface of the inner mitochondrial membrane, overlooking the cytosol, and catalyzes the oxidation of glycerol-3-phosphate to dihydroxyacetone phosphate.
The reactions catalyzed by cytosolic (soluble) and mitochondrial GPDH are as follows:
There are two forms of GPDH:
|EC number||Name||Donor / Acceptor||Name||Subcellular location||Abbreviation||Name||Symbol|
|188.8.131.52||glycerol-3-phosphate dehydrogenase||NADH / NAD+||Glycerol-3-phosphate dehydrogenase [NAD+]||cytoplasmic||GPDH-C||glycerol-3-phosphate dehydrogenase 1 (soluble)||GPD1|
|184.108.40.206||glycerol-3-phosphate dehydrogenase||quinol / quinone||Glycerol-3-phosphate dehydrogenase||mitochondrial||GPDH-M||glycerol-3-phosphate dehydrogenase 2 (mitochondrial)||GPD2|
The following human genes encode proteins with GPDH enzymatic activity:
Cytosolic Glycerol-3-phosphate dehydrogenase (GPD1), is an NAD+-dependent enzyme that reduces dihydroxyacetone phosphate to glycerol-3-phosphate. Simultaneously, NADH is oxidized to NAD+ in the following reaction:
As a result, NAD+ is regenerated for further metabolic activity.
Figure 4. The putative active site. The phosphate group of DHAP is half-encircled by the side-chain of Arg269, and interacts with Arg269 and Gly268 directly by hydrogen bonds (not shown). The conserved residues Lys204, Asn205, Asp260 and Thr264 form a stable hydrogen bonding network. The other hydrogen bonding network includes residues Lys120 and Asp260, as well as an ordered water molecule (with a B-factor of 16.4 Å2), which hydrogen bonds to Gly149 and Asn151 (not shown). In these two electrostatic networks, only the ε-NH3+ group of Lys204 is the nearest to the C2 atom of DHAP (3.4 Å).
Mitochondrial glycerol-3-phosphate dehydrogenase (GPD2), catalyzes the irreversible oxidation of glycerol-3-phosphate to dihydroxyacetone phosphate and concomitantly transfers two electrons from FAD to the electron transport chain. GPD2 consists of 4 identical subunits.
Response to environmental stresses
- Studies indicate that GPDH is mostly unaffected by pH changes: neither GPD1 or GPD2 is favored under certain pH conditions.
- At high salt concentrations (E.g. NaCl), GPD1 activity is enhanced over GPD2, since an increase in the salinity of the medium leads to an accumulation of glycerol in response.
- Changes in temperature do not appear to favor neither GPD1 nor GPD2.
The cytosolic together with the mitochondrial glycerol-3-phosphate dehydrogenase work in concert. Oxidation of cytoplasmic NADH by the cytosolic form of the enzyme creates glycerol-3-phosphate from dihydroxyacetone phosphate. Once the glycerol-3-phosphate has moved through the inner mitochondrial membrane it can then be oxidised by a separate isoform of glycerol-3-phosphate dehydrogenase that uses quinone as an oxidant and FAD as a co-factor. As a result, there is a net loss in energy, comparable to one molecule of ATP.
Role in disease
- Enhanced GPDH activity, particularly GPD2, leads to an increase in glycerol production. Since glycerol is a main subunit in lipid metabolism, its abundance can easily lead to an increase in triglyceride accumulation at a cellular level. As a result, there is a tendency to form adipose tissue leading to an accumulation of fat that favors obesity.
- GPDH has also been found to play a role in Brugada syndrome. Mutations in the gene encoding GPD1 have been proven to cause defects in the electron transport chain. This conflict with NAD+/NADH levels in the cell is believed to contribute to defects in cardiac sodium ion channel regulation and can lead to a lethal arrythmia during infancy.
Glycerol-3-phosphate dehydrogenase consists of two protein domains. The N-terminal domain is an NAD-binding domain, and the C-terminus acts as a substrate-binding domain. However, dimer and tetramer interface residues are involved in GAPDH-RNA binding, as GAPDH can exhibit several moonlighting activities, including the modulation of RNA binding and/or stability.
- substrate pages: glycerol 3-phosphate, dihydroxyacetone phosphate
- related topics: glycerol phosphate shuttle, creatine kinase, glycolysis, gluconeogenesis
- PMID 16460752. doi:10.1016/j.jmb.2005.12.074.; Ou X, Ji C, Han X, Zhao X, Li X, Mao Y, Wong LL, Bartlam M, Rao Z (Mar 2006). "Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1)". Journal of Molecular Biology. 357 (3): 858–69.
- Ou X, Ji C, Han X, Zhao X, Li X, Mao Y, Wong LL, Bartlam M, Rao Z (Mar 2006). "Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1)". Journal of Molecular Biology. 357 (3): 858–69. PMID 16460752. doi:10.1016/j.jmb.2005.12.074.
- Harding JW, Pyeritz EA, Copeland ES, White HB (Jan 1975). "Role of glycerol 3-phosphate dehydrogenase in glyceride metabolism. Effect of diet on enzyme activities in chicken liver" (PDF). The Biochemical Journal. 146 (1): 223–9. PMC . PMID 167714. doi:10.1042/bj1460223.
- Geertman JM, van Maris AJ, van Dijken JP, Pronk JT (Nov 2006). "Physiological and genetic engineering of cytosolic redox metabolism in Saccharomyces cerevisiae for improved glycerol production". Metabolic Engineering. 8 (6): 532–42. PMID 16891140. doi:10.1016/j.ymben.2006.06.004.
- Ansell R, Granath K, Hohmann S, Thevelein JM, Adler L (May 1997). "The two isoenzymes for yeast NAD+-dependent glycerol 3-phosphate dehydrogenase encoded by GPD1 and GPD2 have distinct roles in osmoadaptation and redox regulation". The EMBO Journal. 16 (9): 2179–87. PMC . PMID 9171333. doi:10.1093/emboj/16.9.2179.
- Kota V, Rai P, Weitzel JM, Middendorff R, Bhande SS, Shivaji S (Sep 2010). "Role of glycerol-3-phosphate dehydrogenase 2 in mouse sperm capacitation". Molecular Reproduction and Development. 77 (9): 773–83. PMID 20602492. doi:10.1002/mrd.21218.
- Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2002). "Chapter 18.5: Glycerol 3-Phosphate Shuttle". Biochemistry. San Francisco: W.H. Freeman. ISBN 0-7167-4684-0.
- Guindalini C, Lee KS, Andersen ML, Santos-Silva R, Bittencourt LR, Tufik S (Jan 2010). "The influence of obstructive sleep apnea on the expression of glycerol-3-phosphate dehydrogenase 1 gene". Experimental Biology and Medicine. 235 (1): 52–6. PMID 20404019. doi:10.1258/ebm.2009.009150.
- Bunoust O, Devin A, Avéret N, Camougrand N, Rigoulet M (Feb 2005). "Competition of electrons to enter the respiratory chain: a new regulatory mechanism of oxidative metabolism in Saccharomyces cerevisiae". The Journal of Biological Chemistry. 280 (5): 3407–13. PMID 15557339. doi:10.1074/jbc.M407746200.
- Kota V, Dhople VM, Shivaji S (Apr 2009). "Tyrosine phosphoproteome of hamster spermatozoa: role of glycerol-3-phosphate dehydrogenase 2 in sperm capacitation". Proteomics. 9 (7): 1809–26. PMID 19333995. doi:10.1002/pmic.200800519.
- Kumar S, Kalyanasundaram GT, Gummadi SN (Feb 2011). "Differential response of the catalase, superoxide dismutase and glycerol-3-phosphate dehydrogenase to different environmental stresses in Debaryomyces nepalensis NCYC 3413". Current Microbiology. 62 (2): 382–7. PMID 20644932. doi:10.1007/s00284-010-9717-z.
- Xu SP, Mao XY, Ren FZ, Che HL (Feb 2011). "Attenuating effect of casein glycomacropeptide on proliferation, differentiation, and lipid accumulation of in vitro Sprague-Dawley rat preadipocytes". Journal of Dairy Science. 94 (2): 676–83. PMID 21257036. doi:10.3168/jds.2010-3827.
- Van Norstrand DW, Valdivia CR, Tester DJ, Ueda K, London B, Makielski JC, Ackerman MJ (Nov 2007). "Molecular and functional characterization of novel glycerol-3-phosphate dehydrogenase 1 like gene (GPD1-L) mutations in sudden infant death syndrome". Circulation. 116 (20): 2253–9. PMC . PMID 17967976. doi:10.1161/CIRCULATIONAHA.107.704627.
- Ferrannini E (Oct 2014). "The target of metformin in type 2 diabetes". The New England Journal of Medicine. 371 (16): 1547–8. PMID 25317875. doi:10.1056/NEJMcibr1409796.
- Suresh S, Turley S, Opperdoes FR, Michels PA, Hol WG (May 2000). "A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana". Structure. 8 (5): 541–52. PMID 10801498. doi:10.1016/s0969-2126(00)00135-0.
- White MR, Khan MM, Deredge D, Ross CR, Quintyn R, Zucconi BE, Wysocki VH, Wintrode PL, Wilson GM, Garcin ED (Jan 2015). "A dimer interface mutation in glyceraldehyde-3-phosphate dehydrogenase regulates its binding to AU-rich RNA". The Journal of Biological Chemistry. 290 (3): 1770–85. PMC . PMID 25451934. doi:10.1074/jbc.M114.618165.
- Baranowski T (1963). "α-Glycerophosphate dehydrogenase". In Boyer PD, Lardy H, Myrbäck K. The Enzymes (2nd ed.). New York: Academic Press. pp. 85–96.
- Brosemer RW, Kuhn RW (May 1969). "Comparative structural properties of honeybee and rabbit alpha-glycerophosphate dehydrogenases". Biochemistry. 8 (5): 2095–105. PMID 4307630. doi:10.1021/bi00833a047.
- O'Brien SJ, MacIntyre RJ (Oct 1972). "The -glycerophosphate cycle in Drosophila melanogaster. I. Biochemical and developmental aspects". Biochemical Genetics. 7 (2): 141–61. PMID 4340553. doi:10.1007/BF00486085.
- Warkentin DL, Fondy TP (Jul 1973). "Isolation and characterization of cytoplasmic L-glycerol-3-phosphate dehydrogenase from rabbit-renal-adipose tissue and its comparison with the skeletal-muscle enzyme". European Journal of Biochemistry / FEBS. 36 (1): 97–109. PMID 4200180. doi:10.1111/j.1432-1033.1973.tb02889.x.
- Albertyn J, van Tonder A, Prior BA (Aug 1992). "Purification and characterization of glycerol-3-phosphate dehydrogenase of Saccharomyces cerevisiae". FEBS Letters. 308 (2): 130–2. PMID 1499720. doi:10.1016/0014-5793(92)81259-O.
- Koekemoer TC, Litthauer D, Oelofsen W (Jun 1995). "Isolation and characterization of adipose tissue glycerol-3-phosphate dehydrogenase". The International Journal of Biochemistry & Cell Biology. 27 (6): 625–32. PMID 7671141. doi:10.1016/1357-2725(95)00012-E.
- Påhlman IL, Larsson C, Averét N, Bunoust O, Boubekeur S, Gustafsson L, Rigoulet M (Aug 2002). "Kinetic regulation of the mitochondrial glycerol-3-phosphate dehydrogenase by the external NADH dehydrogenase in Saccharomyces cerevisiae". The Journal of Biological Chemistry. 277 (31): 27991–5. PMID 12032156. doi:10.1074/jbc.M204079200.
- Overkamp KM, Bakker BM, Kötter P, van Tuijl A, de Vries S, van Dijken JP, Pronk JT (May 2000). "In vivo analysis of the mechanisms for oxidation of cytosolic NADH by Saccharomyces cerevisiae mitochondria". Journal of Bacteriology. 182 (10): 2823–30. PMC . PMID 10781551. doi:10.1128/JB.182.10.2823-2830.2000.
- Dawson AG, Cooney GJ (Jul 1978). "Reconstruction of the alpha-glycerolphosphate shuttle using rat kidney mitochondria". FEBS Letters. 91 (2): 169–72. PMID 210038. doi:10.1016/0014-5793(78)81164-8.
- Opperdoes FR, Borst P, Bakker S, Leene W (Jun 1977). "Localization of glycerol-3-phosphate oxidase in the mitochondrion and particulate NAD+-linked glycerol-3-phosphate dehydrogenase in the microbodies of the bloodstream form to Trypanosoma brucei". European Journal of Biochemistry / FEBS. 76 (1): 29–39. PMID 142010. doi:10.1111/j.1432-1033.1977.tb11567.x.
- Eswaramoorthy S, Bonanno JB, Burley SK, Swaminathan S (Jun 2006). "Mechanism of action of a flavin-containing monooxygenase". Proceedings of the National Academy of Sciences of the United States of America. 103 (26): 9832–7. PMC . PMID 16777962. doi:10.1073/pnas.0602398103.
- equivalent entries:
- Yeast genome database GO term: GPDH
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus Provide feedback
NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyses the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the C-terminal substrate-binding domain .
Pahlman IL, Larsson C, Averet N, Bunoust O, Boubekeur S, Gustafsson L, Rigoulet M; , J Biol Chem 2002;277:27991-27995.: Kinetic regulation of the mitochondrial glycerol-3-phosphate dehydrogenase by the external NADH dehydrogenase in Saccharomyces cerevisiae. PUBMED:12032156 EPMC:12032156
Suresh S, Turley S, Opperdoes FR, Michels PA, Hol WG; , Structure Fold Des 2000;8:541-552.: A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana. PUBMED:10801498 EPMC:10801498
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR006109
NAD-dependent glycerol-3-phosphate dehydrogenase (EC) (GPD) catalyzes the reversible reduction of dihydroxyacetone phosphate to glycerol-3-phosphate. It is a cytoplasmic protein, active as a homodimer [PUBMED:2500660], each monomer containing an N-terminal NAD binding site [PUBMED:6773774]. In insects, it acts in conjunction with a mitochondrial alpha-glycerophosphate oxidase in the alpha-glycerophosphate cycle, which is essential for the production of energy used in insect flight [PUBMED:2500660].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|
|Biological process||carbohydrate metabolic process (GO:0005975)|
|oxidation-reduction process (GO:0055114)|
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This helical domain is found associated with Rossmann domains.
The clan contains the following 13 members:3HCDH 6PGD ApbA_C DUF1932 DUF2520 HMD IlvC Mannitol_dh_C NAD_binding_11 NAD_Gly3P_dh_C Octopine_DH P5CR_dimer UDPG_MGDP_dh
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|Author:||Finn RD, Bateman A, Moxon SJ|
|Number in seed:||934|
|Number in full:||5602|
|Average length of the domain:||141.10 aa|
|Average identity of full alignment:||38 %|
|Average coverage of the sequence by the domain:||40.54 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
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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 NAD_Gly3P_dh_C domain has been found. There are 26 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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