Glycerol-3-phosphate dehydrogenase explained

Glycerol-3-phosphate dehydrogenase should not be confused with glyceraldehyde 3-phosphate dehydrogenase.

Glycerol-3-phosphate dehydrogenase (NAD^+)
Ec Number:	1.1.1.8
Cas Number:	9075-65-4
Go Code:	0004367

Glycerol-3-phosphate dehydrogenase (quinone)
Ec Number:	1.1.5.3
Cas Number:	9001-49-4

Symbol:	NAD_Gly3P_dh_N
NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
Pfam:	PF01210
Pfam Clan:	CL0063
Interpro:	IPR011128
Prosite:	PDOC00740
Scop:	1m66

Symbol:	NAD_Gly3P_dh_C
NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
Pfam:	PF07479
Pfam Clan:	CL0106
Interpro:	IPR006109
Prosite:	PDOC00740
Scop:	1m66

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is an enzyme that catalyzes the reversible redox conversion of dihydroxyacetone phosphate (a.k.a. glycerone phosphate, outdated) to sn-glycerol 3-phosphate.^[1]

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.

Metabolic function

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.^[2] Additionally, GPDH is one of the enzymes involved in maintaining the redox potential across the inner mitochondrial membrane.^[2]

Reaction

The NAD+/NADH coenzyme couple act as an electron reservoir for metabolic redox reactions, carrying electrons from one reaction to another.^[3] 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 localized to the outer membrane of the mitochondria facing the 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.^[4]

The reactions catalyzed by cytosolic (soluble) and mitochondrial GPDH are as follows:

Variants

There are two forms of GPDH:

Enzyme			Protein			Gene
EC number	Name	Donor / Acceptor	Name	Subcellular location	Abbreviation	Name	Symbol
1.1.1.8	glycerol-3-phosphate dehydrogenase	NADH / NAD^+	Glycerol-3-phosphate dehydrogenase [NAD<sup>+</sup>]	cytoplasmic	GPDH-C	glycerol-3-phosphate dehydrogenase 1 (soluble)	GPD1
1.1.5.3	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:

glycerol-3-phosphate dehydrogenase 1 (soluble) Hgncid: 4455 Symbol: GPD1 Entrezgene: 2819 Omim: 138420 Refseq: NM_005276 Uniprot: P21695 Ecnumber: 1.1.1.8 Chromosome: 12 Arm: q Band: 12 Locussupplementarydata: -q13

glycerol-3-phosphate dehydrogenase 2 (mitochondrial) Hgncid: 4456 Symbol: GPD2 Entrezgene: 2820 Omim: 138430 Refseq: NM_000408 Uniprot: P43304 Ecnumber: 1.1.5.3 Chromosome: 2 Arm: q Band: 24.1

GPD1

Cytosolic Glycerol-3-phosphate dehydrogenase (GPD1), is an NAD+-dependent enzyme^[5] 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.

GPD1 consists of two subunits,^[6] and reacts with dihydroxyacetone phosphate and NAD+ though the following interaction:

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).

GPD2

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.^[7]

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.^[8]

Glycerol-3-phosphate shuttle

See main article: Glycerol phosphate shuttle.

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 outer 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.

The combined action of these enzymes maintains the NAD+/NADH ratio that allows for continuous operation of metabolism.

Role in disease

The fundamental role of GPDH in maintaining the NAD+/NADH potential, as well as its role in lipid metabolism, makes GPDH a factor in lipid imbalance diseases, such as obesity.

• 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.^[9]
• 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.^[10]

Pharmacological target

The mitochondrial isoform of G3P dehydrogenase is thought to be inhibited by metformin, a first line drug for type 2 diabetes.^[11]

Biological Research

Sarcophaga barbata was used to study the oxidation of L-3-glycerophosphate in mitochondria. It is found that the L-3-glycerophosphate does not enter the mitochondrial matrix, unlike pyruvate. This helps locate the L-3-glycerophosphate-flavoprotein oxidoreductase, which is on the inner membrane of the mitochondria.

Structure

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.^[12] 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.^[13]

See also

• substrate pages: glycerol 3-phosphate, dihydroxyacetone phosphate
• related topics: glycerol phosphate shuttle, creatine kinase, glycolysis, gluconeogenesis

Further reading

• Book: Baranowski T . Boyer PD, Lardy H, Myrbäck K . The Enzymes . 2nd . 1963 . Academic Press . New York . 85–96 . α-Glycerophosphate dehydrogenase .
• Brosemer RW, Kuhn RW . Comparative structural properties of honeybee and rabbit alpha-glycerophosphate dehydrogenases . Biochemistry . 8 . 5 . 2095–105 . May 1969 . 4307630 . 10.1021/bi00833a047 .
• O'Brien SJ, MacIntyre RJ . The -glycerophosphate cycle in Drosophila melanogaster. I. Biochemical and developmental aspects . Biochemical Genetics . 7 . 2 . 141–61 . Oct 1972 . 4340553 . 10.1007/BF00486085 . 22009695 .
• Warkentin DL, Fondy TP . 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 . 36 . 1 . 97–109 . Jul 1973 . 4200180 . 10.1111/j.1432-1033.1973.tb02889.x . free .
• Albertyn J, van Tonder A, Prior BA . Purification and characterization of glycerol-3-phosphate dehydrogenase of Saccharomyces cerevisiae . FEBS Letters . 308 . 2 . 130–2 . Aug 1992 . 1499720 . 10.1016/0014-5793(92)81259-O . 39643279 . free .
• Koekemoer TC, Litthauer D, Oelofsen W . Isolation and characterization of adipose tissue glycerol-3-phosphate dehydrogenase . The International Journal of Biochemistry & Cell Biology . 27 . 6 . 625–32 . Jun 1995 . 7671141 . 10.1016/1357-2725(95)00012-E .
• Påhlman IL, Larsson C, Averét N, Bunoust O, Boubekeur S, Gustafsson L, Rigoulet M . 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 . Aug 2002 . 12032156 . 10.1074/jbc.M204079200 . free .
• Overkamp KM, Bakker BM, Kötter P, van Tuijl A, de Vries S, van Dijken JP, Pronk JT . In vivo analysis of the mechanisms for oxidation of cytosolic NADH by Saccharomyces cerevisiae mitochondria . Journal of Bacteriology . 182 . 10 . 2823–30 . May 2000 . 10781551 . 101991 . 10.1128/JB.182.10.2823-2830.2000 . 10.1.1.335.5313 .
• Dawson AG, Cooney GJ . Reconstruction of the alpha-glycerolphosphate shuttle using rat kidney mitochondria . FEBS Letters . 91 . 2 . 169–72 . Jul 1978 . 210038 . 10.1016/0014-5793(78)81164-8 . free .
• Opperdoes FR, Borst P, Bakker S, Leene W . 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 . 76 . 1 . 29–39 . Jun 1977 . 142010 . 10.1111/j.1432-1033.1977.tb11567.x . free .
• Eswaramoorthy S, Bonanno JB, Burley SK, Swaminathan S . 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 . Jun 2006 . 16777962 . 1502539 . 10.1073/pnas.0602398103 . 2006PNAS..103.9832E . free .

External links

• equivalent entries:
  • • • GPDH
• Yeast genome database GO term: GPDH

Notes and References

1. Ou X, Ji C, Han X, Zhao X, Li X, Mao Y, Wong LL, Bartlam M, Rao Z . Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1) . Journal of Molecular Biology . 357 . 3 . 858–69 . Mar 2006 . 16460752 . 10.1016/j.jmb.2005.12.074 .
2. Harding JW, Pyeritz EA, Copeland ES, White HB . Role of glycerol 3-phosphate dehydrogenase in glyceride metabolism. Effect of diet on enzyme activities in chicken liver . The Biochemical Journal . 146 . 1 . 223–9 . Jan 1975 . 167714 . 1165291 . 10.1042/bj1460223.
3. Ansell R, Granath K, Hohmann S, Thevelein JM, Adler L . 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 . May 1997 . 9171333 . 1169820 . 10.1093/emboj/16.9.2179 .
4. Kota V, Rai P, Weitzel JM, Middendorff R, Bhande SS, Shivaji S . Role of glycerol-3-phosphate dehydrogenase 2 in mouse sperm capacitation . Molecular Reproduction and Development . 77 . 9 . 773–83 . Sep 2010 . 20602492 . 10.1002/mrd.21218 . 19691537 .
5. Guindalini C, Lee KS, Andersen ML, Santos-Silva R, Bittencourt LR, Tufik S . The influence of obstructive sleep apnea on the expression of glycerol-3-phosphate dehydrogenase 1 gene . Experimental Biology and Medicine . 235 . 1 . 52–6 . Jan 2010 . 20404019 . 10.1258/ebm.2009.009150 . 207194967 . 2011-05-16 . https://web.archive.org/web/20110724152256/http://ebm.rsmjournals.com/cgi/content/full/235/1/52 . 2011-07-24 . dead .
6. Bunoust O, Devin A, Avéret N, Camougrand N, Rigoulet M . 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 . Feb 2005 . 15557339 . 10.1074/jbc.M407746200 . free .
7. Kota V, Dhople VM, Shivaji S . Tyrosine phosphoproteome of hamster spermatozoa: role of glycerol-3-phosphate dehydrogenase 2 in sperm capacitation . Proteomics . 9 . 7 . 1809–26 . Apr 2009 . 19333995 . 10.1002/pmic.200800519 . 9248320 .
8. Kumar S, Kalyanasundaram GT, Gummadi SN . 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 . Feb 2011 . 20644932 . 10.1007/s00284-010-9717-z . 41613712 .
9. Xu SP, Mao XY, Ren FZ, Che HL . 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 . Feb 2011 . 21257036 . 10.3168/jds.2010-3827 . free .
10. Van Norstrand DW, Valdivia CR, Tester DJ, Ueda K, London B, Makielski JC, Ackerman MJ . 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 . Nov 2007 . 17967976 . 3332545 . 10.1161/CIRCULATIONAHA.107.704627 .
11. Ferrannini E . The target of metformin in type 2 diabetes . The New England Journal of Medicine . 371 . 16 . 1547–8 . Oct 2014 . 25317875 . 10.1056/NEJMcibr1409796 .
12. Suresh S, Turley S, Opperdoes FR, Michels PA, Hol WG . 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 . May 2000 . 10801498 . 10.1016/s0969-2126(00)00135-0 . free .
13. White MR, Khan MM, Deredge D, Ross CR, Quintyn R, Zucconi BE, Wysocki VH, Wintrode PL, Wilson GM, Garcin ED . A dimer interface mutation in glyceraldehyde-3-phosphate dehydrogenase regulates its binding to AU-rich RNA . en . The Journal of Biological Chemistry . 290 . 3 . 1770–85 . Jan 2015 . 25451934 . 4340419 . 10.1074/jbc.M114.618165 . free .