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Escherichia coli K-12 substr. MG1655 Enzyme: quinoprotein glucose dehydrogenase



Gene: gcd Accession Numbers: EG10369 (EcoCyc), b0124, ECK0123

Regulation Summary Diagram: ?

Summary:
Glucose dehydrogenase (Gcd) is a membrane-bound enzyme. Its role in glucose utilization is not fully clear, because under ordinary conditions it exists as an apoprotein. The enzyme requires the cofactor pyrroloquinoline quinone (PQQ) for activity, yet E. coli lacks the ability to synthesize PQQ [Hommes84, Matsushita97]. However, E. coli exhibits chemotaxis towards environmental PQQ [deJonge96], and may thus use an externally supplied cofactor.

Once functional, the enzyme is able to oxidize glucose and feed electrons into the respiratory chain [vanSchie85], but does not generate a proton motive force [Yamada93]. The topological structure of Gcd within the membrane has been investigated and revealed five N-terminal membrane-spanning segments, with the N terminus located in the cytoplasm and the C terminus is located in the periplasm [Yamada93]. The C-terminal periplasmic domain binds PQQ, contains the catalytic activity and is able to interact with ubiquinone in the cytoplasmic membrane [Elias01]. A ubiquinone-interacting site is located close to the membrane surface [Miyoshi99].

Further experiments showed that Gcd contains two ubiquinone binding sites [Elias04]. In addition to the PQQ cofactor, a tightly bound ubiquinone-8 molecule is located very close to PQQ at an estimated distance of 11-13 Å [Elias04, Kobayashi05] and mediates the electron transfer from PQQ to the membrane ubiquinone pools [Kobayashi05, Mustafa08]. Menaquinone can substitute for ubiquinone in this function [Mustafa08a]. Bound ubiquinone and may be involved in the oxidation of glucose in addition to the intramolecular electron transfer from PQQ [Mustafa08b, Mustafa08a]. The residues thought to interact with PQQ and the bound ubiquinone have been identified by site-directed mutagenesis [Yamada98b, Elias00, Mustafa08]. The specificity for Mg2+ as the metal cofactor has been studied [James03].

A gcd insertion mutant has no detectable growth rate defect; however, in a strain with a phosphotransferase system mutation and in the presence of the PQQ cofactor, a gcd mutant can no longer utilize glucose as the sole source of carbon [CletonJansen90]. Overexpression of Gcd may alter sugar utilization preferences [Sode95]. Expression of gcd is increased in the presence of glucose and under aerobic growth conditions [Yamada93a] and may be repressed by FNR [Constantinidou06].

Combined site-directed mutagenesis and homology modeling studies of E. coli Gcd have suggested that conserved amino acid residues Asp204 and Gly776 are functionally important [Sashidhar10].

Review: [Yamada03a]

Citations: [Cozier95]

Locations: periplasmic space, inner membrane

Map Position: [138,835 <- 141,225] (2.99 centisomes)
Length: 2391 bp / 796 aa

Molecular Weight of Polypeptide: 86.747 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0000433 , CGSC:30502 , DIP:DIP-9747N , EchoBASE:EB0364 , EcoGene:EG10369 , EcoliWiki:b0124 , Mint:MINT-1267882 , OU-Microarray:b0124 , PortEco:gcd , PR:PRO_000022760 , Pride:P15877 , Protein Model Portal:P15877 , RefSeq:NP_414666 , RegulonDB:EG10369 , SMR:P15877 , String:511145.b0124 , UniProt:P15877

Relationship Links: InterPro:IN-FAMILY:IPR001479 , InterPro:IN-FAMILY:IPR002372 , InterPro:IN-FAMILY:IPR011047 , InterPro:IN-FAMILY:IPR017511 , InterPro:IN-FAMILY:IPR018391 , InterPro:IN-FAMILY:IPR027295 , Pfam:IN-FAMILY:PF01011 , Prosite:IN-FAMILY:PS00363 , Prosite:IN-FAMILY:PS00364 , Smart:IN-FAMILY:SM00564

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0019595 - non-phosphorylated glucose catabolic process Inferred from experiment [CletonJansen90]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [James03]
GO:0008876 - quinoprotein glucose dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA01a, Yamada93]
GO:0048039 - ubiquinone binding Inferred from experiment [Elias04]
GO:0070968 - pyrroloquinoline quinone binding Inferred from experiment [Yamada98b]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors Inferred by computational analysis [GOA01]
GO:0048038 - quinone binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0016021 - integral component of membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Yamada93]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Yamada93]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [GOA01]

MultiFun Terms: cell structure membrane
metabolism carbon utilization carbon compounds
metabolism central intermediary metabolism misc. glucose metabolism
metabolism energy production/transport electron donors

Essentiality data for gcd 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 Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Curated 24-Nov-2009 by Keseler I , SRI International
Last-Curated ? 17-Mar-2010 by Fulcher C , SRI International


Enzymatic reaction of: glucose dehydrogenase

Alternative Substrates for D-glucopyranose: 3-deoxy-D-glucose [Cozier99 ] , D-allose [Cozier99 ] , 2-deoxy-D-glucose [Cozier99 ] , 6-deoxy-D-glucose [Cozier99 ] , D-fucose [Cozier99 ] , melibiose [Cozier99 ] , D-glucosamine [Cozier99 ] , α-D-xylopyranose [Cozier99 ] , D-galactose [Cozier99 ]

In Pathways: glucose and glucose-1-phosphate degradation

Summary:
Kinetic studies of PQQ and Mg2+ binding have been performed [Yamada98b, Cozier99, Iswantini00]. The substrate specificity of the enzyme was investigated by [Cozier99].

Cofactors or Prosthetic Groups: ubiquinone-8 [Elias04], pyrroloquinoline quinone [Yamada98b], Mg2+ [Yamada98b, James03, Cozier99]

Inhibitors (Competitive): L-ribose [Cozier99] , D-arabinose [Cozier99] , α-D-lyxopyranose [Cozier99] , L-xylose [Cozier99]

Kinetic Parameters:

Substrate
Km (μM)
Citations
D-glucopyranose
750.0
[Yamada98b]

T(opt): 25 °C [BRENDA14, Southall06]

pH(opt): 7 [BRENDA14, Southall06]


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 11 -> 37
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Transmembrane-Region 41 -> 58
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Sequence-Conflict 59
[CletonJansen90, UniProt10a]
Alternate sequence: R → L; UniProt: (in Ref. 1; CAA35706);
Transmembrane-Region 63 -> 81
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Transmembrane-Region 96 -> 110
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Transmembrane-Region 119 -> 141
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Sequence-Conflict 149 -> 156
[Yamada93a, CletonJansen90, UniProt10a]
Alternate sequence: TLSADATP → HLKRRCHT; UniProt: (in Ref. 1 and 2);
Sequence-Conflict 193
[Yamada93a, CletonJansen90, UniProt10a]
Alternate sequence: N → K; UniProt: (in Ref. 1 and 2);
Active-Site 466
[UniProt10]
UniProt: Proton acceptor; Non-Experimental Qualifier: probable;
Sequence-Conflict 666
[Yamada93a, UniProt10a]
Alternate sequence: Q → H; UniProt: (in Ref. 2; BAA02174);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0124 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10369; 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

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

CletonJansen90: Cleton-Jansen AM, Goosen N, Fayet O, van de Putte P (1990). "Cloning, mapping, and sequencing of the gene encoding Escherichia coli quinoprotein glucose dehydrogenase." J Bacteriol 172(11);6308-15. PMID: 2228962

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Cozier95: Cozier GE, Anthony C (1995). "Structure of the quinoprotein glucose dehydrogenase of Escherichia coli modelled on that of methanol dehydrogenase from Methylobacterium extorquens." Biochem J 312 ( Pt 3);679-85. PMID: 8554505

Cozier99: Cozier GE, Salleh RA, Anthony C (1999). "Characterization of the membrane quinoprotein glucose dehydrogenase from Escherichia coli and characterization of a site-directed mutant in which histidine-262 has been changed to tyrosine." Biochem J 1999;340 ( Pt 3);639-47. PMID: 10359647

deJonge96: de Jonge R, Teixeira de Mattos MJ, Stock JB, Neijssel OM (1996). "Pyrroloquinoline quinone, a chemotactic attractant for Escherichia coli." J Bacteriol 178(4);1224-6. PMID: 8576064

Elias00: Elias MD, Tanaka M, Izu H, Matsushita K, Adachi O, Yamada M (2000). "Functions of amino acid residues in the active site of Escherichia coli pyrroloquinoline quinone-containing quinoprotein glucose dehydrogenase." J Biol Chem 275(10);7321-6. PMID: 10702303

Elias01: Elias M, Tanaka M, Sakai M, Toyama H, Matsushita K, Adachi O, Yamada M (2001). "C-terminal periplasmic domain of Escherichia coli quinoprotein glucose dehydrogenase transfers electrons to ubiquinone." J Biol Chem 276(51);48356-61. PMID: 11604400

Elias04: Elias MD, Nakamura S, Migita CT, Miyoshi H, Toyama H, Matsushita K, Adachi O, Yamada M (2004). "Occurrence of a bound ubiquinone and its function in Escherichia coli membrane-bound quinoprotein glucose dehydrogenase." J Biol Chem 279(4);3078-83. PMID: 14612441

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

Geiger87: Geiger O, Gorisch H (1987). "Enzymatic determination of pyrroloquinoline quinone using crude membranes from Escherichia coli." Anal Biochem 164(2);418-23. PMID: 3118738

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.

Hommes84: Hommes RWJ, Postma PW, Neijssel OM, Tempest DW, Dokter P, Duine JA (1984). "Evidence for a glucose dehydrogenase apoenzyme in several strains of Escherichia coli." FEMS Microbiol Lett 24;329-333.

Iswantini00: Iswantini D, Kano K, Ikeda T (2000). "Kinetics and thermodynamics of activation of quinoprotein glucose dehydrogenase apoenzyme in vivo and catalytic activity of the activated enzyme in Escherichia coli cells." Biochem J 350 Pt 3;917-23. PMID: 10970809

James03: James PL, Anthony C (2003). "The metal ion in the active site of the membrane glucose dehydrogenase of Escherichia coli." Biochim Biophys Acta 1647(1-2);200-5. PMID: 12686133

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

Kobayashi05: Kobayashi K, Mustafa G, Tagawa S, Yamada M (2005). "Transient formation of a neutral ubisemiquinone radical and subsequent intramolecular electron transfer to pyrroloquinoline quinone in the Escherichia coli membrane-integrated glucose dehydrogenase." Biochemistry 44(41);13567-72. PMID: 16216080

Matsushita97: Matsushita K, Arents JC, Bader R, Yamada M, Adachi O, Postma PW (1997). "Escherichia coli is unable to produce pyrroloquinoline quinone (PQQ)." Microbiology 143 ( Pt 10);3149-56. PMID: 9353919

Miyoshi99: Miyoshi H, Niitome Y, Matsushita K, Yamada M, Iwamura H (1999). "Topographical characterization of the ubiquinone reduction site of glucose dehydrogenase in Escherichia coli using depth-dependent fluorescent inhibitors." Biochim Biophys Acta 1412(1);29-36. PMID: 10354491

Mustafa08: Mustafa G, Ishikawa Y, Kobayashi K, Migita CT, Elias MD, Nakamura S, Tagawa S, Yamada M (2008). "Amino acid residues interacting with both the bound quinone and coenzyme, pyrroloquinoline quinone, in Escherichia coli membrane-bound glucose dehydrogenase." J Biol Chem 283(32);22215-21. PMID: 18550551

Mustafa08a: Mustafa G, Migita CT, Ishikawa Y, Kobayashi K, Tagawa S, Yamada M (2008). "Menaquinone as well as ubiquinone as a bound quinone crucial for catalytic activity and intramolecular electron transfer in Escherichia coli membrane-bound glucose dehydrogenase." J Biol Chem 283(42);28169-75. PMID: 18708350

Mustafa08b: Mustafa G, Ishikawa Y, Kobayashi K, Migita CT, Tagawa S, Yamada M (2008). "Function of a bound ubiquinone in Escherichia coli quinoprotein glucose dehydrogenase." Biofactors 32(1-4);23-9. PMID: 19096097

Sashidhar10: Sashidhar B, Inampudi KK, Guruprasad L, Kondreddy A, Gopinath K, Podile AR (2010). "Highly Conserved Asp-204 and Gly-776 Are Important for Activity of the Quinoprotein Glucose Dehydrogenase of Escherichia coli and for Mineral Phosphate Solubilization." J Mol Microbiol Biotechnol 18(2);109-119. PMID: 20215780

Sode95: Sode K, Sugimoto S, Watanabe M, Tsugawa W (1995). "Effect of PQQ glucose dehydrogenase overexpression in Escherichia coli on sugar-dependent respiration." J Biotechnol 43(1);41-4. PMID: 8573321

Southall06: Southall SM, Doel JJ, Richardson DJ, Oubrie A (2006). "Soluble aldose sugar dehydrogenase from Escherichia coli: a highly exposed active site conferring broad substrate specificity." J Biol Chem 281(41);30650-9. PMID: 16864586

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 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."

vanSchie85: van Schie BJ, Hellingwerf KJ, van Dijken JP, Elferink MG, van Dijl JM, Kuenen JG, Konings WN (1985). "Energy transduction by electron transfer via a pyrrolo-quinoline quinone-dependent glucose dehydrogenase in Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter calcoaceticus (var. lwoffi)." J Bacteriol 163(2);493-9. PMID: 3926746

Yamada03a: Yamada M, Elias MD, Matsushita K, Migita CT, Adachi O (2003). "Escherichia coli PQQ-containing quinoprotein glucose dehydrogenase: its structure comparison with other quinoproteins." Biochim Biophys Acta 1647(1-2);185-92. PMID: 12686131

Yamada93: Yamada M, Sumi K, Matsushita K, Adachi O, Yamada Y (1993). "Topological analysis of quinoprotein glucose dehydrogenase in Escherichia coli and its ubiquinone-binding site." J Biol Chem 268(17);12812-7. PMID: 8509415

Yamada93a: Yamada M, Asaoka S, Saier MH, Yamada Y (1993). "Characterization of the gcd gene from Escherichia coli K-12 W3110 and regulation of its expression." J Bacteriol 1993;175(2);568-71. PMID: 8419307

Yamada98b: Yamada M, Inbe H, Tanaka M, Sumi K, Matsushita K, Adachi O (1998). "Mutant isolation of the Escherichia coli quinoprotein glucose dehydrogenase and analysis of crucial residues Asp-730 and His-775 for its function." J Biol Chem 273(34);22021-7. PMID: 9705344

Other References Related to Gene Regulation

Izu02: Izu H, Ito S, Elias MD, Yamada M (2002). "Differential control by IHF and cAMP of two oppositely oriented genes, hpt and gcd, in Escherichia coli: significance of their partially overlapping regulatory elements." Mol Genet Genomics 266(5);865-72. PMID: 11810262


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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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