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



Gene: glpD Accession Numbers: EG10394 (EcoCyc), b3426, ECK3412

Synonyms: glyD, glycerol-3-phosphate oxidase

Regulation Summary Diagram: ?

Subunit composition of glycerol-3-phosphate dehydrogenase, aerobic = [GlpD]2

Summary:
glpD encodes aerobic glycerol 3-phosphate dehydrogenase [Schweizer87, Austin91] which catalyses the oxidation of glycerol-3-phosphate to dihydroxyacetone phosphate. GlpD is a respiratory enzyme and shuttles electrons via a noncovalently bound FAD cofactor to reduce ubiquinone [Schryvers78, Yeh08].

Mutants lacking glpD are unable to grow on glycerol or glycerol-3-phosphate [Cozzarelli65]. Glycerol-3-phosphate is an obligatory intermediate in phospholipid biosynthesis and thus glpD expression is regulated to ensure that phospholipid biosynthesis is maintained while the energy needs of the cell are met. Expression of glpD (along with other members of the glp regulon) is repressed by GlpR and induced by glycerol-3-phosphate [Cozzarelli68, Lin76]. Anaerobically glpD expression is repressed by the two-component regulatory system arcA and arcB [Iuchi90]. Both ubiquinone and menaquinone restore glycerol-3-phosphate oxidase activity in membranes isolated from an E. coli strain lacking quinones (ubiA- menA-) [Wallace77].

GlpD is a homodimeric enzyme associated with the cytoplasmic membrane through binding to negatively-charged phopholipids [Walz02]. GlpD is composed of two domains, the soluble extramembranous C-terminal "cap" domain and a membrane-bound N-terminal domain which binds FAD and glycerol-3-phosphate and is also thought to be the ubiquinone docking domain [Yeh08]. Seven fully active structures of GlpD in the native state and with bound substrate analogues have been solved to at least 1.75 Å resolution [Yeh08].

E. coli K-12 contains two glycerol-3-phosphate dehydrogenases encoded by the glpD and glpABC genes. GlpD is required for aerobic growth with glycerol or glycerol-3-phosphate while GlpABC is required for anaerobic growth with glycerol (or glycerol-3-phosphate) and fumarate. Either enzyme suffices for anaerobic growth on glycerol and nitrate (see [Kistler71, Miki75a] and review by [Stewart88]). The ratio of GlpD to GlpABC is high when oxygen or nitrate serves as a terminal electron acceptor and low when fumarate serves this role [Freedberg73].

Citations: [Weiner72, Robinson80]

Gene Citations: [Persson00]

Locations: cytosol, inner membrane

Map Position: [3,560,036 -> 3,561,541] (76.73 centisomes)
Length: 1506 bp / 501 aa

Molecular Weight of Polypeptide: 56.751 kD (from nucleotide sequence), 58.0 kD (experimental) [Schryvers78 ]

pI: 6.33

Unification Links: ASAP:ABE-0011191 , CGSC:693 , DIP:DIP-9793N , EchoBASE:EB0389 , EcoGene:EG10394 , EcoliWiki:b3426 , Mint:MINT-1248675 , ModBase:P13035 , OU-Microarray:b3426 , PortEco:glpD , PR:PRO_000022795 , Pride:P13035 , Protein Model Portal:P13035 , RefSeq:NP_417884 , RegulonDB:EG10394 , SMR:P13035 , String:511145.b3426 , UniProt:P13035

Relationship Links: InterPro:IN-FAMILY:IPR000447 , InterPro:IN-FAMILY:IPR006076 , PDB:Structure:2QCU , PDB:Structure:2R45 , PDB:Structure:2R46 , PDB:Structure:2R4E , PDB:Structure:2R4J , Pfam:IN-FAMILY:PF01266 , Prints:IN-FAMILY:PR01001 , Prosite:IN-FAMILY:PS00977 , Prosite:IN-FAMILY:PS00978

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009060 - aerobic respiration Inferred from experiment [Kistler71]
GO:0009061 - anaerobic respiration Inferred from experiment [Kistler71]
GO:0046168 - glycerol-3-phosphate catabolic process Inferred from experiment [Cozzarelli65]
GO:0006071 - glycerol metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006072 - glycerol-3-phosphate metabolic process Inferred by computational analysis [GOA01a]
GO:0019563 - glycerol catabolic process Inferred by computational analysis [UniProtGOA12]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0009055 - electron carrier activity Inferred from experiment [Schryvers78]
GO:0042803 - protein homodimerization activity Inferred from experiment [Yeh08]
GO:0052590 - sn-glycerol-3-phosphate:ubiquinone oxidoreductase activity Inferred by computational analysis Inferred from experiment [Schryvers78, Yeh08]
GO:0071949 - FAD binding Inferred from experiment [Schryvers78]
GO:0004368 - glycerol-3-phosphate dehydrogenase activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0052591 - sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment [Schryvers78]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Schryvers78]
GO:0009331 - glycerol-3-phosphate dehydrogenase complex Inferred from experiment Inferred by computational analysis [GOA01a, Yeh08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolism central intermediary metabolism misc. glycerol metabolism
metabolism energy metabolism, carbon aerobic respiration
metabolism energy production/transport electron donors

Essentiality data for glpD 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 Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 3]

Credits:
Last-Curated ? 05-Aug-2014 by Mackie A , Macquarie University


Enzymatic reaction of: glycerol-3-phosphate dehydrogenase, aerobic

Synonyms: G3P dehydrogenase, sn-glycerol-3-phosphate:(acceptor) 2-oxidoreductase

EC Number: 1.1.5.3

In Pathways: glycerol and glycerophosphodiester degradation , glycerol degradation I , glycerophosphodiester degradation , glycerol-3-phosphate to cytochrome bo oxidase electron transfer

Cofactor Binding Comment: The enzyme contains 0.5 mol of FAD/mol of monomer [Schryvers78]

Inhibitors (Competitive): dihydroxyacetone phosphate [Schryvers78] , 3-phospho-D-glycerate [Schryvers78] , 2-phospho-D-glycerate [Schryvers78] , D-glyceraldehyde 3-phosphate [Schryvers78] , 2-phosphoglycolate [Schryvers78] , phosphoenolpyruvate [Schryvers78]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
sn-glycerol 3-phosphate
100.0, 339.0
33.3
[Schryvers81, BRENDA14]

T(opt): 44 °C [BRENDA14, Schryvers78]

pH(opt): 7 [BRENDA14, Schryvers78]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 5 -> 33
[UniProt10]
UniProt: FAD; Non-Experimental Qualifier: potential;
Sequence-Conflict 23
[Choi89, UniProt10a]
Alternate sequence: A → G; UniProt: (in Ref. 2; BAA00327);
Sequence-Conflict 328 -> 353
[Choi89, UniProt10a]
Alternate sequence: QAITRDYTLDIHDENGKAPLLSVFGG → HVLPVITPLIFMMKMAKHRCCRYSAA; UniProt: (in Ref. 2; BAA00327);
Sequence-Conflict 464 -> 501
[Choi89, UniProt10a]
Alternate sequence: DDALWRRTKQGMWLNADQQSRVSQWLVEYTQQRLSLAS → ARRPVASHKTRHVAKCGSTISCESVAGGVYAAEVIAGVVN; UniProt: (in Ref. 2; BAA00327);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3426 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10394; confirmed by SwissProt match.


References

Austin91: Austin D, Larson TJ (1991). "Nucleotide sequence of the glpD gene encoding aerobic sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12." J Bacteriol 1991;173(1);101-7. PMID: 1987111

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

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

Choi89: Choi Y.-L., Kawase S., Kawamukai M., Utsumi R., Sakai H., Komano T. (1989). "Nucleotide sequence of the glycerol-3-phosphate dehydrogenase gene of Escherichia coli and regulation by the cAMP-CRP complex." Agric. Biol. Chem., Volume 53, page(s) 1135-1143.

Cozzarelli65: Cozzarelli NR, Koch JP, Hayashi S, Lin EC (1965). "Growth stasis by accumulated L-alpha-glycerophosphate in Escherichia coli." J Bacteriol 90(5);1325-9. PMID: 5321485

Cozzarelli68: Cozzarelli NR, Freedberg WB, Lin EC (1968). "Genetic control of L-alpha-glycerophosphate system in Escherichia coli." J Mol Biol 31(3);371-87. PMID: 4866330

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Freedberg73: Freedberg WB, Lin EC (1973). "Three kinds of controls affecting the expression of the glp regulon in Escherichia coli." J Bacteriol 115(3);816-23. PMID: 4580569

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Iuchi90: Iuchi S, Cole ST, Lin EC (1990). "Multiple regulatory elements for the glpA operon encoding anaerobic glycerol-3-phosphate dehydrogenase and the glpD operon encoding aerobic glycerol-3-phosphate dehydrogenase in Escherichia coli: further characterization of respiratory control." J Bacteriol 1990;172(1);179-84. PMID: 2403539

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kistler71: Kistler WS, Lin EC (1971). "Anaerobic L- -glycerophosphate dehydrogenase of Escherichia coli: its genetic locus and its physiological role." J Bacteriol 108(3);1224-34. PMID: 4945192

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

Miki75a: Miki K, Lin EC (1975). "Electron transport chain from glycerol 3-phosphate to nitrate in Escherichia coli." J Bacteriol 124(3);1288-94. PMID: 127786

Persson00: Persson M, Glatz E, Rutberg B (2000). "Different processing of an mRNA species in Bacillus subtilis and Escherichia coli." J Bacteriol 182(3);689-95. PMID: 10633102

Robinson80: Robinson JJ, Weiner JH (1980). "The effect of amphipaths on the flavin-linked aerobic glycerol-3-phosphate dehydrogenase from Escherichia coli." Can J Biochem 58(10);1172-8. PMID: 6780164

Schryvers78: Schryvers A, Lohmeier E, Weiner JH (1978). "Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli." J Biol Chem 253(3);783-8. PMID: 340460

Schryvers81: Schryvers A, Weiner JH (1981). "The anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli. Purification and characterization." J Biol Chem 1981;256(19);9959-65. PMID: 6792201

Schweizer87: Schweizer H, Larson TJ (1987). "Cloning and characterization of the aerobic sn-glycerol-3-phosphate dehydrogenase structural gene glpD of Escherichia coli K-12." J Bacteriol 1987;169(2);507-13. PMID: 3027031

Stewart88: Stewart V (1988). "Nitrate respiration in relation to facultative metabolism in enterobacteria." Microbiol Rev 52(2);190-232. PMID: 3045516

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

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

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

Wallace77: Wallace BJ, Young IG (1977). "Role of quinones in electron transport to oxygen and nitrate in Escherichia coli. Studies with a ubiA- menA- double quinone mutant." Biochim Biophys Acta 461(1);84-100. PMID: 195602

Walz02: Walz AC, Demel RA, de Kruijff B, Mutzel R (2002). "Aerobic sn-glycerol-3-phosphate dehydrogenase from Escherichia coli binds to the cytoplasmic membrane through an amphipathic alpha-helix." Biochem J 365(Pt 2);471-9. PMID: 11955283

Weiner72: Weiner JH, Heppel LA (1972). "Purification of the membrane-bound and pyridine nucleotide-independent L-glycerol 3-phosphate dehydrogenase from Escherichia coli." Biochem Biophys Res Commun 47(6);1360-5. PMID: 4557172

Yeh08: Yeh JI, Chinte U, Du S (2008). "Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism." Proc Natl Acad Sci U S A 105(9);3280-5. PMID: 18296637

Other References Related to Gene Regulation

BeckerHapak95: Becker-Hapak M, Eisenstark A (1995). "Role of rpoS in the regulation of glutathione oxidoreductase (gor) in Escherichia coli." FEMS Microbiol Lett 134(1);39-44. PMID: 8593953

Weissenborn92: Weissenborn DL, Wittekindt N, Larson TJ (1992). "Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12." J Biol Chem 1992;267(9);6122-31. PMID: 1372899

Yang96: Yang B, Larson TJ (1996). "Action at a distance for negative control of transcription of the glpD gene encoding sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12." J Bacteriol 178(24);7090-8. PMID: 8955388

Ye88: Ye SZ, Larson TJ (1988). "Structures of the promoter and operator of the glpD gene encoding aerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12." J Bacteriol 1988;170(9);4209-15. PMID: 3045087

Zhao94: Zhao N, Oh W, Trybul D, Thrasher KS, Kingsbury TJ, Larson TJ (1994). "Characterization of the interaction of the glp repressor of Escherichia coli K-12 with single and tandem glp operator variants." J Bacteriol 176(8);2393-7. PMID: 8157609


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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 Dec 20, 2014, BIOCYC13B.