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Escherichia coli K-12 substr. MG1655 Enzyme: glycerol-3-phosphate dehydrogenase, biosynthetic



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

Regulation Summary Diagram: ?

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] (81.49 centisomes)
Length: 1020 bp / 339 aa

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: ?

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

Essentiality data for gpsA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Credits:
Last-Curated ? 06-Sep-2011 by Keseler I , 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

dihydroxyacetone 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: phospholipid biosynthesis I , CDP-diacylglycerol biosynthesis II , CDP-diacylglycerol biosynthesis I

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]
dihydroxyacetone phosphate
170.0
[Kito69, BRENDA14]
dihydroxyacetone 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
[UniProt10a]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 110
[UniProt10a]
UniProt: NAD; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 143
[UniProt10a]
UniProt: NAD; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Active-Site 195
[UniProt10a]
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 259
[UniProt10a]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Protein-Segment 259 -> 260
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 285
[UniProt10a]
UniProt: NAD; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

UniProt10a: 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 EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Nov 22, 2014, BIOCYC14A.