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MetaCyc Enzyme: glycerol-3-phosphate dehydrogenase, biosynthetic

Gene: gpsA Accession Numbers: EG20091 (MetaCyc), b3608, ECK3598

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of glycerol-3-phosphate dehydrogenase, biosynthetic = [GpsA]2
         glycerol-3-phosphate dehydrogenase = GpsA

Summary:
Glycerol-3-phosphate dehydrogenase (GpsA) catalyzes the NAD(P)H-dependent reduction of the glycolytic intermediate dihydroxyacetone-phosphate to produce glycerol-3-phosphate, a precursor for the biosynthesis of phospholipids [Hsu70, Bell74, Cronan74, Edgar79].

GpsA activity is strongly inhibited in vitro by glycerol-3-phosphate, and it was shown that this inhibition does not involve dimer association or dissociation. A mutant version of the protein which is resistant to feedback inhibition has been studied [Bell75].

The enzyme is constitutively produced, and is present in the cell in low amounts. It was calculated that on average only about 1000 molecules are present per cell [Edgar78].

GpsA did not show dehydrogenase activity in a high-throughput screen of purified proteins [Kuznetsova05].

Locations: cytosol

Map Position: [3,780,665 <- 3,781,684]

Molecular Weight of Polypeptide: 36.362 kD (from nucleotide sequence), 32.5 kD (experimental) [Edgar78 ]

Molecular Weight of Multimer: 49 kD (experimental) [Edgar78]

pI: 6.0 [Edgar78, Edgar78]

Unification Links: ASAP:ABE-0011795 , CGSC:663 , DIP:DIP-48003N , EchoBASE:EB4142 , EcoGene:EG20091 , EcoliWiki:b3608 , ModBase:P0A6S7 , OU-Microarray:b3608 , PortEco:gpsA , PR:PRO_000022833 , Pride:P0A6S7 , Protein Model Portal:P0A6S7 , RefSeq:NP_418065 , RegulonDB:EG20091 , SMR:P0A6S7 , String:511145.b3608 , UniProt:P0A6S7

Relationship Links: InterPro:IN-FAMILY:IPR006109 , InterPro:IN-FAMILY:IPR006168 , InterPro:IN-FAMILY:IPR008927 , InterPro:IN-FAMILY:IPR011128 , InterPro:IN-FAMILY:IPR013328 , InterPro:IN-FAMILY:IPR016040 , Panther:IN-FAMILY:PTHR11728 , Pfam:IN-FAMILY:PF01210 , Pfam:IN-FAMILY:PF07479 , Prints:IN-FAMILY:PR00077 , Prosite:IN-FAMILY:PS00957

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Instance reaction of [sn-glycerol 3-phosphate + NAD(P)+ ← glycerone phosphate + NAD(P)H + H+] (1.1.1.94):
i1: sn-glycerol 3-phosphate + NAD+ ↔ glycerone phosphate + NADH + H+ (1.1.1.8)

GO Terms:

Biological Process: GO:0046474 - glycerophospholipid biosynthetic process Inferred from experiment [Hsu70, Bell74, Cronan74]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01]
GO:0006072 - glycerol-3-phosphate metabolic process Inferred by computational analysis [GOA01]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0006650 - glycerophospholipid metabolic process Inferred by computational analysis [UniProtGOA12]
GO:0008654 - phospholipid biosynthetic process Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0046167 - glycerol-3-phosphate biosynthetic process Inferred by computational analysis [GOA06]
GO:0046168 - glycerol-3-phosphate catabolic process Inferred by computational analysis [GOA01]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0042803 - protein homodimerization activity Inferred from experiment [Edgar78]
GO:0047952 - glycerol-3-phosphate dehydrogenase [NAD(P)+] activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Cronan74, Edgar78]
GO:0004367 - glycerol-3-phosphate dehydrogenase [NAD+] activity Inferred by computational analysis [GOA01a, GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01]
GO:0036439 - glycerol-3-phosphate dehydrogenase [NADP+] activity Inferred by computational analysis [GOA01a]
GO:0050662 - coenzyme binding Inferred by computational analysis [GOA01]
GO:0051287 - NAD binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]
GO:0009331 - glycerol-3-phosphate dehydrogenase complex Inferred by computational analysis [GOA01]

MultiFun Terms: metabolism central intermediary metabolism misc. glycerol metabolism
metabolism metabolism of other compounds phosphorous metabolism

Credits:
Imported from EcoCyc 27-Jan-2015 by Paley S , SRI International


Enzymatic reaction of: glycerol-3-phosphate dehydrogenase

Synonyms: sn-glycerol-3-phosphate:NAD(P)+ 2-oxidoreductase, glycerol-3-phosphate-dehydrogenase-[NAD(P)+]

EC Number: 1.1.1.94

glycerone phosphate + NAD(P)H + H+ <=> sn-glycerol 3-phosphate + NAD(P)+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: 1,3-propanediol biosynthesis (engineered) , superpathway of phospholipid biosynthesis I (bacteria) , CDP-diacylglycerol biosynthesis I , CDP-diacylglycerol biosynthesis II

Credits:
Imported from EcoCyc 27-Jan-2015 by Paley S , SRI International

Summary:
The enzyme was initially purified from E. coli B [Kito69].

Glycerol phosphate is a competitive inhibitor with respect to dihydroxyacetone phosphate [Edgar78a].

Cofactor Binding Comment: The coenzyme requirement is not strict. [Lin76]

Inhibitors (Competitive): sn-glycerol 3-phosphate (Kic = 4.4µM) [Clark80a, Edgar78a]

Inhibitors (Noncompetitive): palmitoyl-CoA (Ki = 1µM) [Edgar79]

Inhibitors (Unknown Mechanism): a long-chain acyl-CoA [Edgar79]

Primary Physiological Regulators of Enzyme Activity: sn-glycerol 3-phosphate

Kinetic Parameters:

Substrate
Km (μM)
Vmax (µmol mg-1 min-1)
Citations
NAD(P)H
3.4
[Edgar78a]
sn-glycerol 3-phosphate
210.0
[Kito69, BRENDA14]
sn-glycerol 3-phosphate
30.0
[Edgar78a]
NAD(P)+
165.0
[Edgar78a]
glycerone phosphate
170.0
[Kito69, BRENDA14]
glycerone phosphate
180.0
78.0
[Edgar78a]

pH(opt): 7.4 [BRENDA14, Kito69], 7.2 [Edgar78a]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 12 -> 17
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 110
[UniProt10]
UniProt: NAD; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 143
[UniProt10]
UniProt: NAD; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Active-Site 195
[UniProt10]
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 259
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Protein-Segment 259 -> 260
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 285
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;

History:
10/20/97 Gene b3608 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG20091; confirmed by SwissProt match.


References

Bell74: Bell RM (1974). "Mutants of Escherichia coli defective in membrane phospholipid synthesis: macromolecular synthesis in an sn-glycerol 3-phosphate acyltransferase Km mutant." J Bacteriol 117(3);1065-76. PMID: 4591941

Bell75: Bell RM, Cronan JE (1975). "Mutants of Escherichia coli defective in membrane phospholipid synthesis. Phenotypic suppression of sn-glycerol-3-phosphate acyltransferase Km mutants by loss of feedback inhibition of the biosynthetic sn-glycerol-3-phosphate dehydrogenase." J Biol Chem 250(18);7153-8. PMID: 240817

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Clark80a: Clark D, Lightner V, Edgar R, Modrich P, Cronan JE, Bell RM (1980). "Regulation of phospholipid biosynthesis in Escherichia coli. Cloning of the structural gene for the biosynthetic sn-glycerol-3-phosphate dehydrogenase." J Biol Chem 255(2);714-7. PMID: 6985897

Cronan74: Cronan JE, Bell RM (1974). "Mutants of Escherichia coli defective in membrane phospholipid synthesis: mapping of the structural gene for L-glycerol 3-phosphate dehydrogenase." J Bacteriol 118(2);598-605. PMID: 4597451

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Edgar78: Edgar JR, Bell RM (1978). "Biosynthesis in Escherichia coli fo sn-glycerol 3-phosphate, a precursor of phospholipid." J Biol Chem 1978;253(18);6348-53. PMID: 355254

Edgar78a: Edgar JR, Bell RM (1978). "Biosynthesis in Escherichia coli of sn-glycerol 3-phosphate, a precursor of phospholipid. Kinetic characterization of wild type and feedback-resistant forms of the biosynthetic sn-glycerol-3-phosphate dehydrogenase." J Biol Chem 253(18);6354-63. PMID: 28326

Edgar79: Edgar JR, Bell RM (1979). "Biosynthesis in Escherichia coli of sn-glycerol 3-phosphate, a precursor of phospholipid. Palmitoyl-CoA inhibition of the biosynthetic sn-glycerol-3-phosphate dehydrogenase." J Biol Chem 1979;254(4);1016-21. PMID: 368067

Edgar80: Edgar JR, Bell RM (1980). "Biosynthesis in Escherichia coli of sn-glycerol-3-phosphate, a precursor of phospholipid. Further kinetic characterization of wild type and feedback-resistant forms of the biosynthetic sn-glycerol-3-phosphate dehydrogenase." J Biol Chem 255(8);3492-7. PMID: 6767719

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hsu70: Hsu CC, Fox CF (1970). "Induction of the lactose transport system in a lipid-synthesis-defective mutant of Escherichia coli." J Bacteriol 103(2);410-6. PMID: 4914567

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Kito69: Kito M, Pizer LI (1969). "Purification and regulatory properties of the biosynthetic L-glycerol 3-phosphate dehydrogenase from Escherichia coli." J Biol Chem 244(12);3316-23. PMID: 4389388

Kuznetsova05: Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF (2005). "Enzyme genomics: Application of general enzymatic screens to discover new enzymes." FEMS Microbiol Rev 29(2);263-79. PMID: 15808744

Lin76: Lin EC (1976). "Glycerol dissimilation and its regulation in bacteria." Annu Rev Microbiol 1976;30;535-78. PMID: 825019

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.0 on Wed May 6, 2015, biocyc14.