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Escherichia coli K-12 substr. MG1655 Polypeptide: anaerobic glycerol-3-phosphate dehydrogenase subunit C




Gene: glpC Accession Numbers: EG10393 (EcoCyc), b2243, ECK2235

Regulation Summary Diagram

Regulation summary diagram for glpC

Component of: glycerol-3-phosphate dehydrogenase, anaerobic (extended summary available)

Summary:
GlpC is the membrane associated subunit of the heterotrimeric glycerol-3-phosphate dehydrogenase complex. In anaerobic conditions this respiratory enzyme converts glycerol-3-phosphate to dihydroxyacetone phosphate (DHAP) using fumarate a a terminal electron acceptor. Overexpressed GlpC associates with the inner membrane [Varga95]. GlpC contains two cysteine clusters typical of iron-sulfur binding domains [Cole88, Varga95].

[Varga95] uses the name GlpB for the protein encoded by the third gene in the glp operon.

Citations: [Shimizu05, Lan03]

Gene Citations: [Larson92, Ehrmann87]

Locations: cytosol, inner membrane

Map Position: [2,353,543 -> 2,354,733] (50.73 centisomes, 183°)
Length: 1191 bp / 396 aa

Molecular Weight of Polypeptide: 44.108 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007426, CGSC:17692, DIP:DIP-35835N, EchoBASE:EB0388, EcoGene:EG10393, EcoliWiki:b2243, ModBase:P0A996, OU-Microarray:b2243, PortEco:glpC, PR:PRO_000022794, Pride:P0A996, Protein Model Portal:P0A996, RefSeq:NP_416746, RegulonDB:EG10393, SMR:P0A996, String:511145.b2243, UniProt:P0A996

Relationship Links: InterPro:IN-FAMILY:IPR004017, InterPro:IN-FAMILY:IPR009051, InterPro:IN-FAMILY:IPR017753, InterPro:IN-FAMILY:IPR017896, InterPro:IN-FAMILY:IPR017900, Pfam:IN-FAMILY:PF02754, Pfam:IN-FAMILY:PF13183, Prosite:IN-FAMILY:PS00198, Prosite:IN-FAMILY:PS51379

In Paralogous Gene Group: 393 (2 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for glpC


GO Terms:
Biological Process:
Inferred from experimentGO:0009061 - anaerobic respiration [Kuritzkes84]
Inferred from experimentGO:0022900 - electron transport chain [Varga95]
Inferred from experimentGO:0046168 - glycerol-3-phosphate catabolic process [Varga95]
Inferred by computational analysisGO:0006810 - transport [GOA01a]
Inferred by computational analysisGO:0019563 - glycerol catabolic process [UniProtGOA12]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0004368 - glycerol-3-phosphate dehydrogenase activity [Varga95]
Inferred from experimentInferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a, Varga95]
Inferred from experimentInferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a, GOA01a, Cole88, Varga95]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, Varga95, Zhang07, LopezCampistrou05]
Inferred from experimentGO:0009331 - glycerol-3-phosphate dehydrogenase complex [Varga95]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, GOA01a]

MultiFun Terms: cell structuremembrane
metabolismcentral intermediary metabolismmisc. glycerol metabolism
metabolismenergy metabolism, carbonanaerobic respiration
metabolismenergy production/transportelectron donors

Essentiality data for glpC knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated 28-Oct-2013 by Kubo A, SRI International


Subunit of: glycerol-3-phosphate dehydrogenase, anaerobic

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

Subunit composition of glycerol-3-phosphate dehydrogenase, anaerobic = [GlpA][GlpB][GlpC]
         anaerobic glycerol-3-phosphate dehydrogenase subunit A = GlpA (summary available)
         anaerobic glycerol-3-phosphate dehydrogenase subunit B = GlpB (summary available)
         anaerobic glycerol-3-phosphate dehydrogenase subunit C = GlpC (summary available)

Summary:
glpABC encodes anaerobic glycerol-3-phosphate dehydrogenase which catalyses the oxidation of glycerol-3-phosphate to dihyroxyacetone phosphate. GlpABC is a respiratory enzyme; anaerobic growth of E. coli with glycerol and fumarate induces expression of an anaerobic glycerol-3-phosphate dehydrogenase and fumarate reductase and is associated with proton translocation and the generation of a proton motive force [Miki78, Miki73, Kistler71].

The GlpABC enzyme is loosely associated with the cell membrane. A functional two subunit form, GlpAB, has been isolated and characterised; it is assumed that the third subunit (GlpC) is responsible for membrane anchoring. The GlpAB complex contains contains 1 molecule of FAD and 2 non-haem irons per dimer; the GlpB subunit is thought to bind flavin mononucleotide [Schryvers81, Cole88]. The GlpC subunit contains two iron-sulfur binding sites; it does not contain any transmembrane helices, so the mechanism by which it acts as the membrane anchor for the complex is not clear [Cole88, Varga95]. Overexpressed GlpC associates with the inner membrane. GlpC is a participant in the electron transport path ( [Varga95] - note that this paper uses the name GlpB for the protein encoded by the third gene in the glp operon).

glpABC is subject to complex transcriptional regulation. Expression of glpABC (along with other members of the glp regulon) is repressed by GlpR and induced by glycerol-3-phosphate; the glp regulon is subject to catabolite repression during growth in the presence of glucose (reviewed in [Lin76], [Larson92] ). Expression of glpABC is positively regulated by the the Fnr transcription regulator [Kuritzkes84, Iuchi90].

E. coli K-12 contains two glycerol-3-phosphate dehydrogenases encoded by the glpABC and glpD genes. GlpABC is required for anaerobic growth with glycerol or glycerol-3-phosphate and fumarate as the terminal electron acceptor while GlpD is required for aerobic growth with glycerol (or glycerol-3-phosphate). Either enzyme suffices for anaerobic growth on glycerol and nitrate ( [Kistler71, Miki75] 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: [Yang97]

Locations [ Comment 5]: cytosol


GO Terms:
Biological Process:
Inferred from experimentGO:0009061 - anaerobic respiration [Kistler71, Miki78]
Inferred from experimentGO:0046168 - glycerol-3-phosphate catabolic process [Schryvers81]
Molecular Function:
Inferred from experimentGO:0004368 - glycerol-3-phosphate dehydrogenase activity [Schryvers81]
Inferred from experimentGO:0050660 - flavin adenine dinucleotide binding [Schryvers81]
Cellular Component:
Inferred from experimentGO:0009331 - glycerol-3-phosphate dehydrogenase complex [Varga95]

Credits:
Last-Curated 06-Aug-2014 by Mackie A, Macquarie University


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

Inferred from experiment

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

EC Number: 1.1.5.3

Transport reaction diagram for glycerol-3-phosphate dehydrogenase, anaerobic

In Pathways: glycerol and glycerophosphodiester degradation, glycerol degradation I, glycerophosphodiester degradation, nitrate reduction IX (dissimilatory), glycerol-3-phosphate to fumarate electron transfer

Cofactors or Prosthetic Groups: a [FeS] iron-sulfur cluster [Varga95], FAD [Schryvers81], FMN [Schryvers81]

Inhibitors (Unknown Mechanism): p-chloromercuriphenylsulfonate [Schryvers81], 5,5'-dithio-bis-2-nitrobenzoate [Schryvers81]Kinetic Parameters:
Substrate Km (μM) kcat (sec-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

Protein sequence of anaerobic glycerol-3-phosphate dehydrogenase subunit C with features indicated

Feature Class Location Citations Comment
Conserved-Region 2 -> 29
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 1.
Metal-Binding-Site 9
Inferred by computational analysis[UniProt10a, Cole88]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 12
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 15
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Metal-Binding-Site 19
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Conserved-Region 45 -> 76
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type 2.
Metal-Binding-Site 56
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 59
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 62
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 2 (4Fe-4S).
Metal-Binding-Site 66
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur 1 (4Fe-4S).
Sequence-Conflict 169
Inferred by curator[Cole88, UniProt15]
UniProt: (in Ref. 1; AAA83866).
Sequence-Conflict 206
Inferred by curator[Cole88, UniProt15]
UniProt: (in Ref. 1; AAA83866).


Sequence Pfam Features

Protein sequence of anaerobic glycerol-3-phosphate dehydrogenase subunit C with features indicated

Feature Class Location Citations Comment
Pfam PF13183 6 -> 70
Inferred by computational analysis[Finn14]
Fer4_8 : 4Fe-4S dicluster domain
Pfam PF02754 163 -> 249
Inferred by computational analysis[Finn14]
CCG : Cysteine-rich domain
Pfam PF02754 293 -> 376
Inferred by computational analysis[Finn14]
CCG : Cysteine-rich domain


Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b2243 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10393; 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

Bairoch93: Bairoch A, Boeckmann B (1993). "The SWISS-PROT protein sequence data bank, recent developments." Nucleic Acids Res. 21:3093-3096. PMID: 8332529

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Cole88: Cole ST, Eiglmeier K, Ahmed S, Honore N, Elmes L, Anderson WF, Weiner JH (1988). "Nucleotide sequence and gene-polypeptide relationships of the glpABC operon encoding the anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12." J Bacteriol 1988;170(6);2448-56. PMID: 3286606

Ehrmann87: Ehrmann M, Boos W, Ormseth E, Schweizer H, Larson TJ (1987). "Divergent transcription of the sn-glycerol-3-phosphate active transport (glpT) and anaerobic sn-glycerol-3-phosphate dehydrogenase (glpA glpC glpB) genes of Escherichia coli K-12." J Bacteriol 169(2);526-32. PMID: 3027032

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

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

Kuritzkes84: Kuritzkes DR, Zhang XY, Lin EC (1984). "Use of phi(glp-lac) in studies of respiratory regulation of the Escherichia coli anaerobic sn-glycerol-3-phosphate dehydrogenase genes (glpAB)." J Bacteriol 157(2);591-8. PMID: 6363389

Lan03: Lan J, Newman EB (2003). "A requirement for anaerobically induced redox functions during aerobic growth of Escherichia coli with serine, glycine and leucine as carbon source." Res Microbiol 154(3);191-7. PMID: 12706508

Larson92: Larson TJ, Cantwell JS, van Loo-Bhattacharya AT (1992). "Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12." J Biol Chem 1992;267(9);6114-21. PMID: 1556120

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

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Miki73: Miki K, Lin EC (1973). "Enzyme complex which couples glycerol-3-phosphate dehydrogenation to fumarate reduction in Escherichia coli." J Bacteriol 114(2);767-71. PMID: 4574699

Miki75: 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

Miki78: Miki K, Wilson TH (1978). "Proton translocation associated with anaerobic transhydrogenation from glycerol 3-phosphate to fumarate in Escherichia coli." Biochem Biophys Res Commun 83(4);1570-5. PMID: 29636

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

Shimizu05: Shimizu K, Hayashi S, Kako T, Suzuki M, Tsukagoshi N, Doukyu N, Kobayashi T, Honda H (2005). "Discovery of glpC, an organic solvent tolerance-related gene in Escherichia coli, using gene expression profiles from DNA microarrays." Appl Environ Microbiol 71(2);1093-6. PMID: 15691972

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." 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."

Varga95: Varga ME, Weiner JH (1995). "Physiological role of GlpB of anaerobic glycerol-3-phosphate dehydrogenase of Escherichia coli." Biochem Cell Biol 73(3-4);147-53. PMID: 7576488

Yang97: Yang B, Gerhardt SG, Larson TJ (1997). "Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K-12." Mol Microbiol 24(3);511-21. PMID: 9179845

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Bradley07: Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (2007). "Effects of Fis on Escherichia coli gene expression during different growth stages." Microbiology 153(Pt 9);2922-40. PMID: 17768236

Pruss01: Pruss BM, Liu X, Hendrickson W, Matsumura P (2001). "FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions." FEMS Microbiol Lett 2001;197(1);91-7. PMID: 11287152

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

Wong92a: Wong KK, Kwan HS (1992). "Transcription of glpT of Escherichia coli K12 is regulated by anaerobiosis and fnr." FEMS Microbiol Lett 1992;73(1-2);15-8. PMID: 1521763

Zhao94a: 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

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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