Biology:Glycerol-3-phosphate dehydrogenase

Short description: Class of enzymes

Glycerol-3-phosphate dehydrogenase (NAD+)
Crystallographic structure of human glycerol-3-phosphate dehydrogenase 1.
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 / QuickGO
Search PMC articles PubMed articles NCBI proteins

Glycerol-3-phosphate dehydrogenase (quinone)
Identifiers
EC number	1.1.5.3
CAS number	9001-49-4
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
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
SCOP2	1m66 / SCOPe / SUPFAM
Available protein structures: Pfam   structures / ECOD   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
SCOP2	1m66 / SCOPe / SUPFAM
Available protein structures: Pfam   structures / ECOD   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is an enzyme that catalyzes the reversible redox conversion of dihydroxyacetone phosphate (a.k.a. glycerone phosphate, outdated) to sn-glycerol 3-phosphate.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.

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

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 at 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.

Reaction

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 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.

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. 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:

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+]	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) Identifiers Symbol GPD1 NCBI gene 2819 HGNC 4455 OMIM 138420 RefSeq NM_005276 UniProt P21695 Other data EC number 1.1.1.8 Locus Chr. 12 q12-q13

glycerol-3-phosphate dehydrogenase 2 (mitochondrial) Identifiers Symbol GPD2 NCBI gene 2820 HGNC 4456 OMIM 138430 RefSeq NM_000408 UniProt P43304 Other data EC number 1.1.5.3 Locus Chr. 2 q24.1

GPD1

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:

GPD1 Reaction Mechanism

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

GPD1 consists of two subunits, 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.

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.

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 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.
• 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.

Pharmacological target

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

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. 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.

See also

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

Further reading

• Baranowski T (1963). "α-Glycerophosphate dehydrogenase". The Enzymes (2nd ed.). New York: Academic Press. pp. 85–96. 
• "Comparative structural properties of honeybee and rabbit alpha-glycerophosphate dehydrogenases". Biochemistry 8 (5): 2095–105. May 1969. doi:10.1021/bi00833a047. PMID 4307630. 
• "The -glycerophosphate cycle in Drosophila melanogaster. I. Biochemical and developmental aspects". Biochemical Genetics 7 (2): 141–61. Oct 1972. doi:10.1007/BF00486085. PMID 4340553. 
• "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. doi:10.1111/j.1432-1033.1973.tb02889.x. PMID 4200180. 
• "Purification and characterization of glycerol-3-phosphate dehydrogenase of Saccharomyces cerevisiae". FEBS Letters 308 (2): 130–2. Aug 1992. doi:10.1016/0014-5793(92)81259-O. PMID 1499720. 
• "Isolation and characterization of adipose tissue glycerol-3-phosphate dehydrogenase". The International Journal of Biochemistry & Cell Biology 27 (6): 625–32. Jun 1995. doi:10.1016/1357-2725(95)00012-E. PMID 7671141. 
• "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. doi:10.1074/jbc.M204079200. PMID 12032156. http://www.jbc.org/content/277/31/27991.full. 
• "In vivo analysis of the mechanisms for oxidation of cytosolic NADH by Saccharomyces cerevisiae mitochondria". Journal of Bacteriology 182 (10): 2823–30. May 2000. doi:10.1128/JB.182.10.2823-2830.2000. PMID 10781551. 
• "Reconstruction of the alpha-glycerolphosphate shuttle using rat kidney mitochondria". FEBS Letters 91 (2): 169–72. Jul 1978. doi:10.1016/0014-5793(78)81164-8. PMID 210038. 
• "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. doi:10.1111/j.1432-1033.1977.tb11567.x. PMID 142010. 
• "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. doi:10.1073/pnas.0602398103. PMID 16777962. Bibcode: 2006PNAS..103.9832E. 

External links

• equivalent entries:
  • alphaGPDH at the US National Library of Medicine Medical Subject Headings (MeSH)
  • GPDH
• Yeast genome database GO term: GPDH

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

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