Glycerol-3-phosphate dehydrogenase

Glycerol-3-phosphate dehydrogenase (NAD+)
Crystallographic structure of human glycerol-3-phosphate dehydrogenase 1.[4]
Identifiers
EC number	1.1.1.8
CAS number	9075-65-4
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
Gene Ontology	AmiGO / EGO
Search PMC articles PubMed articles NCBI proteins

NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
crystal structure of the n-(1-d-carboxylethyl)-l-norvaline dehydrogenase from arthrobacter sp. strain 1c
Identifiers
Symbol	NAD_Gly3P_dh_N
Pfam	PF01210
Pfam clan	CL0063
InterPro	IPR011128
PROSITE	PDOC00740
SCOP	1m66
SUPERFAMILY	1m66
Available protein structures: Pfam structures PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
structure of glycerol-3-phosphate dehydrogenase from archaeoglobus fulgidus
Identifiers
Symbol	NAD_Gly3P_dh_C
Pfam	PF07479
Pfam clan	CL0106
InterPro	IPR006109
PROSITE	PDOC00740
SCOP	1m66
SUPERFAMILY	1m66
Available protein structures: Pfam structures PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Glycerol-3-phosphate dehydrogenase (GPDH) is an enzyme that catalyzes the reversible redox conversion of dihydroxyacetone phosphate (aka glycerone phosphate, outdated) to sn-glycerol 3-phosphate.^[5]

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.^[6] Additionally, GPDH is responsible for maintaining the redox potential across the inner mitochondrial membrane in glycolysis.^[6]

Fig. 1. Schematic overview of fermentative and oxidative glucose metabolism of Saccharomyces cerevisiae. (A) upper part of glycolysis, which includes two sugar phosphorylation reactions. (B) fructose-1,6-bisphosphate aldolase, splitting the C6-molecule into two triose phosphates (C) triosephosphate isomerase, interconverting DHAP and GAP. (D) glycerol pathway reducing DHAP to glycerol-3-phosphate (G3P) by G3P dehydrogenase, followed by dephosphorylation to glycerol by G3Pase. (E) The lower part of glycolysis converts GAP to pyruvate while generating 1 NADH and 2 ATP via a series of 5 enzymes. (F) Alcoholic fermentation; decarboxylation of pyruvate by pyruvate decarboxylase, followed by reduction of acetaldehyde to ethanol. (G) mitochondrial pyruvate-dehydrogenase converts pyruvate to acetyl-CoA, which enters the tricarboxylic acid cycle. (H) external mitochondrial NADH dehydrogenases. (I) mitochondrial G3P dehydrogenase. Electrons of these three dehydrogenases enter the respiratory chain that the level of the quinol pool (Q). (J) internal mitochondrial NADH dehydrogenase. (K) ATP synthase. (L) generalized scheme of NADH shuttle. (M) formate oxidation by formate dehydrogenase.^[2]

Reaction

The NAD+/NADH coenzyme couple act as an electron reservoir for metabolic redox reactions, carrying electrons from one reaction to another.^[7] 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.^[2]

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.^[8]

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

Coupled reactions catalyzed by the cytosolic (GPDH-C) and mitochondrial (GPDH-M) forms of glycerol 3-phosphate dehydrogenase.[1] GPDH-C and GPDH-M use NADH and quinol (QH) as an electron donors respectively. GPDH-M in addition uses FAD as a co-factor.

Variants

There are two forms of GPDH:

The following human genes encode proteins with GPDH enzymatic activity:

GPD1

Cytosolic Glycerol-3-phosphate dehydrogenase (GPD1), is an NAD+-dependent enzyme^[9] that reduces dihydroxyacetone phosphate to glycerol-3-phosphate. Simultaneously, NADH is oxidized to NAD+ in the following reaction:

GPD1 Reaction Mechanism

As a result, NAD+ is regenerated for further metabolic activity.

GPD1 consists of two subunits,^[10] 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).^[4]

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.^[11]

X-ray structure of glycerol-3-phosphate dehydrogenase from Bacilius halodurans complexed with FAD. Northeast Structural Genomics Consortium target BhR167.^[3]

GPD2 Reaction Mechanism

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.^[12]

Glycerol-3-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 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.^[1]

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 GDPH in maintaining the NAD+/NADH potential, as well as its role in lipid metabolism, makes GDPH 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.^[13]

• 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.^[14]

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.^[15]

See also

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

References

Further reading

• 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.  Cite uses deprecated parameters (help)
• 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.  Cite uses deprecated parameters (help)
• 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.  Cite uses deprecated parameters (help); |accessdate= requires |url= (help)
• 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.  Cite uses deprecated parameters (help); |accessdate= requires |url= (help)
• 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.  Cite uses deprecated parameters (help)

External links

• equivalent entries:
  • alphaGPDH at the US National Library of Medicine Medical Subject Headings (MeSH)
  • GPDH
• Yeast genome database GO term: GPDH
• enzyme no. -2053504966 at GPnotebook

This article incorporates text from the public domain Pfam and InterPro IPR011128

This article incorporates text from the public domain Pfam and InterPro IPR006109