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 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 responsible for maintaining the redox potential across the inner mitochondrial membrane in glycolysis.
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.
- substrate pages: glycerol 3-phosphate, dihydroxyacetone phosphate
- related topics: glycerol phosphate shuttle, creatine kinase, glycolysis, gluconeogenesis
- PDB 1X0V; Ou X, Ji C, Han X, Zhao X, Li X, Mao Y, Wong LL, Bartlam M, Rao Z (March 2006). "Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1)". J. Mol. Biol. 357 (3): 858–69. doi:10.1016/j.jmb.2005.12.074. PMID 16460752.
- Ou, Xianjin; Ji Chaoneng, Han Xueqing, Zhao Xiaodong, Li Xuemei, Mao Yumin, Wong Luet-Lok, Bartlam Mark, Rao Zihe (31 March 2006). "Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1)". Journal of Molecular Biology 357 (3): 858–869. doi:10.1016/j.jmb.2005.12.074. PMID 16460752. Retrieved 14 May 2011.
- Harding Jr., Joseph W.; Pyeritz, Eric A.; Copeland, Eric S.; White III, Harold B. (1975). "Role of Glycerol 3-Phosphate Dehydrogenase in Glyceride Metabolism - Effect of Diet on Enzyme Activities in Chicken Liver". Biochem Journal 146: 223–229.
- Geertman, Jan-Maarten A.; van Maris, Antonius J.A.; van Dijken, Johannes P.; Rronk, Jack T. (November 2006). "Physiological and genetic engineering of cytosolic redox metabolism in Saccharomyces cerevisiae for improved glycerol production". Metabolic Engineering 8 (6): 532–542. doi:10.1016/j.ymben.2006.06.004. PMID 16891140. Retrieved 14 May 2011.
- Ansell, Ricky; Granath, Katarina ; Hohmann, Stefan ; Thevelein, Johan M. and Adler, Lennart (14 January 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): 2179–2187. doi:10.1093/emboj/16.9.2179. PMC 1169820. PMID 9171333. Retrieved 15 May 2011.
- Kota, Venkatesh; Rai, Priyanka; Weitzel, Joachim m.; Middendorff, Ralf; Bhande, Satish S.; Shivaji, Sisinthy (2 July 2010). "Role of glycerol-3-phosphate dehydrogenase 2 in mouse sperm capacitation". Molecular Reproduction and Development 77 (9): 773–783. doi:10.1002/mrd.21218/full. PMID 20602492.
- 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, Camila; Lee, Kil S.; Andersen, Monica L.; Santos-Silva, Rogerio; Bittencourt, Lia Rita A. and Tufik, Sergio (2010). "The influence of obstructive sleep apnea on the expression of glycerol-3-phosphate dehydrogenase1 gene". Experimental Biology and Medicine 235 (1): 52–56. doi:10.1258/ebm.2009.009150. PMID 20404019.
- Bunoust, Odile; Devin, Anne; Averet, Nicole; Camougrand, Nadine and Rigoulet, Michel (4 February 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): 3407–3413. doi:10.1074/jbc.M407746200. PMID 15557339. Retrieved 16 May 2011.
- Kota, Venkatesh; Dhople, Vishnu M. and Shivaji, Sisinthy (2009). "Tyrosine phosphoproteome of hamster spermatozoa: Role of glycerol-3-phosphate dehydrogenase 2 in sperm capacitation". Proteomics 9 (7): 1809–1826. doi:10.1002/pmic.200800519. PMID 200800519.
- Kuzin, A.P. "X-Ray structure of the glycerol-3-phosphate dehydrogenase from Bacillus halodurans complexed with FAD. Northeast Structural Genomics Consortium target BhR167.". www.pdb.org. Retrieved 16 May 2011.
- Kumar, Sawan; Kalyanasundaram, Gayathiri T. and Gummadi, Sathyanarayana N. (20 July 2010). "Differential Response of the Catalase, Superoxide Dismutase and Glycerol-3-phosphate Dehydrogenase to Different Environmental Stresses in Debaryomyces nepalensis NCYC 3413". Journal of industrial microbiology & biotechnology.
- Xu, S.P; Mao, X.Y.; Ren, F.Z. and Che, H.L. (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): 676–683. doi:10.3168/jds.2010-3827. PMID 21257036.
- Van Norstrand, David W.; Validivia, Carmen R.; Tester, David J; Ueda, Kazuo; London, Barry; Makielski, Jonthan C and Ackerman, michael J. (14 May 2011). "Molecular and Functional Characterization of Novel Glycerol-3-Phosphate Dehydroogenase 1 like Gene (GPD1-L) Mutations in Sudden Infant Death Syndrome". Journal of the American Heart Association 116 (20): 2253–9. doi:10.1161/CIRCULATIONAHA.107.704627. PMID 17967976. Retrieved 18 May 2011.
- 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.
- 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 α-glycerophosphate dehydrogenases". Biochemistry 8 (5): 2095–105. doi:10.1021/bi00833a047. PMID 4307630.
- O'Brien SJ, MacIntyre RJ (October 1972). "The -glycerophosphate cycle in Drosophila melanogaster. I. Biochemical and developmental aspects". Biochem. Genet. 7 (2): 141–61. doi:10.1007/BF00486085. PMID 4340553.
- Warkentin DL, Fondy TP (July 1973). "Isolation and characterization of cytoplasmic L-glycerol-3-phosphate dehydrogenase from rabbit-renal-adipose tissue and its comparison with the skeletal-muscle enzyme". Eur. J. Biochem. 36 (1): 97–109. doi:10.1111/j.1432-1033.1973.tb02889.x. PMID 4200180.
- Albertyn J, van Tonder A, Prior BA (August 1992). "Purification and characterization of glycerol-3-phosphate dehydrogenase of Saccharomyces cerevisiae". FEBS Lett. 308 (2): 130–2. doi:10.1016/0014-5793(92)81259-O. PMID 1499720.
- Koekemoer TC, Litthauer D, Oelofsen W (June 1995). "Isolation and characterization of adipose tissue glycerol-3-phosphate dehydrogenase". Int. J. Biochem. Cell Biol. 27 (6): 625–32. doi:10.1016/1357-2725(95)00012-E. PMID 7671141.
- Pahlman, Inga-lill; Larsson, Christer; Averet, Nicole; Bunoust, Odile; Boubekeur, Samira; Gustafsson, Lena and Rigoulet, Michel (2 August 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): 27991–27995. doi:10.1074/jbc.M204079200. PMID 12032156.
- Overkamp, Karin M.; Bakker, Barbara M.; Kotter, Peter; van Tuijl, Arjen; de Vries, Simon; van Dijken, Johannes P. and Pronk, Jack T. (May 2000). "In Vivo Analysis of the Mechanisms for Oxidation of Cytosolic NADH by Saccharomyces cerevisiae Mitochondria". Journal of Bacteriology 182 (10): 2823–2830. doi:10.1128/JB.182.10.2823-2830.2000. PMC 101991. PMID 10781551. Retrieved 16 May 2011.
- Dawson, Anthony G.; Cooney, Gregory J. (July 1978). "RECONSTRUCTION OF THE wGLYCEROLPHOSPHATE SHUTTLE USING RAT KIDNEY MITOCHONDRIA". Febs Letters 91 (2): 169–172. doi:10.1016/0014-5793(78)81164-8. PMID 210038.
- Opperdoes, Fred R.; Borst, Piet; Bakker, Suzanne and Leene, Wolter (18 October 1976). "Localization of Glycerol-3-Phosphate Oxidase in the Mitochondrion and Particulate NAD+-Linked Glycerol-3-Phosphate Dehydrogenase in the Microbodies of the Bloodstream Form of Trypanosoma brucei". European Journal of Biochemistry 76 (1): 29–39. doi:10.1111/j.1432-1033.1977.tb11567.x. PMID 142010.
- Eswaramoorthy, Subramaniam; Bonanno, Jeffrey B.; Burley, Stephen K. and Swaminathan, Subramanyam (15 June 2006). "Mechanism of action of a flavin-containing monooxygenase". Proceedings of the National Academy of Sciences of the United States of America 103 (26): 9832–9837. doi:10.1073/pnas.0602398103. PMC 1502539. PMID 16777962. Retrieved 16 May 2011.
- equivalent entries:
- Yeast genome database GO term: GPDH
- enzyme no. -2053504966 at GPnotebook
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||oxidoreductase activity, acting on CH-OH group of donors (GO:0016614)|
|Biological process||carbohydrate metabolic process (GO:0005975)|
|oxidation-reduction process (GO:0055114)|
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|Author:||Finn RD, Bateman A, Moxon SJ|
|Number in seed:||27|
|Number in full:||5512|
|Average length of the domain:||143.50 aa|
|Average identity of full alignment:||41 %|
|Average coverage of the sequence by the domain:||42.43 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
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We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 22 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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