EzCatDB: S00165

DB codeS00165
CATH domainDomain 12.120.10.30Catalytic domain
E.C.1.1.5.2
CSA1c9u
MACiEM0104


Enzyme Name
Swiss-protKEGG

P13650
Protein nameQuinoprotein glucose dehydrogenase Bquinoprotein glucose dehydrogenase
D-glucose:(pyrroloquinoline-quinone) 1-oxidoreductase
glucose dehydrogenase (PQQ-dependent)
glucose dehydrogenase (pyrroloquinoline-quinone)
quinoprotein D-glucose dehydrogenase
SynonymsEC 1.1.5.2
Glucose dehydrogenase B [pyrroloquinoline-quinone]
Soluble glucose dehydrogenase
s-GDH

KEGG pathways
MAP codePathways
MAP00030Pentose phosphate pathway

Swiss-prot:Accession NumberP13650
Entry nameDHGB_ACICA
ActivityD-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol.
SubunitHomodimer.
Subcellular location
CofactorBinds 1 PQQ group per subunit.,Binds 3 calcium ions per subunit.


CofactorsSubstratesProducts
KEGG-idC00113C00076C00031C00399C00198C00390
CompoundPQQCalciumD-GlucoseUbiquinoneD-Glucono-1,5-lactoneUbiquinol
Typearomatic ring (with nitrogen atoms),carbohydrate,carboxyl groupdivalent metal (Ca2+, Mg2+)carbohydratearomatic ring (only carbon atom),carbohydrate,lipidcarbohydratearomatic ring (only carbon atom),carbohydrate,lipid
1c9uABound:PQQBound:_CA 1003UnboundUnboundUnboundUnbound
1c9uBBound:PQQBound:_CA 1003UnboundUnboundUnboundUnbound
1cq1ABound:PQQBound:_CA 503Bound:GLCUnboundUnboundUnbound
1cq1BBound:PQQBound:_CA 503Bound:GLCUnboundUnboundUnbound
1cruABound:PQQBound:_CA 909UnboundUnboundUnboundUnbound
1cruBAnalogue:PQQ-HDNBound:_CA 908UnboundUnboundUnboundUnbound
1qbiAUnboundBound:_CA 468UnboundUnboundUnboundUnbound
1qbiBUnboundBound:_CA 467UnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P13650 & literature [13]
pdbCatalytic residuesCofactor-binding residues
1c9uAHIS 144;ASP 163
GLY 247;PRO 248(Calcium binding)
1c9uBHIS 144;ASP 163
GLY 247;PRO 248(Calcium binding)
1cq1AHIS 144;ASP 163
GLY 247;PRO 248(Calcium binding)
1cq1BHIS 144;ASP 163
GLY 247;PRO 248(Calcium binding)
1cruAHIS 144;ASP 163
GLY 247;PRO 248(Calcium binding)
1cruBHIS 144;ASP 163
GLY 247;PRO 248(Calcium binding)
1qbiAHIS 144;ASP 163
GLY 247;PRO 248(Calcium binding)
1qbiBHIS 144;ASP 163
GLY 247;PRO 248(Calcium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Scheme 4
[5]Fig.2, p.5192
[7]Fig.2, p.11791
[8]Scheme 3, p.9390-9391
[9]FIG. 8, p.769
[10]Fig. 2, p.144-145
[13]Scheme 1, Chart 3, p.2437-2438

references
[1]
PubMed ID2820412
JournalBiochem Biophys Res Commun
Year1987
Volume147
Pages701-9
AuthorsNagasawa T, Yamada H
TitleNitrile hydratase is a quinoprotein. A possible new function of pyrroloquinoline quinone: activation of H2O in an enzymatic hydration reaction.
[2]
PubMed ID8411180
JournalJ Mol Biol
Year1993
Volume233
Pages784-6
AuthorsSchlunegger MP, Grutter MG, Streiff MB, Olsthoorn AJ, Duine JA
TitleCrystallization and preliminary crystallographic investigations of the soluble glucose dehydrogenase from Acinetobacter calcoaceticus.
[3]
PubMed ID8951033
JournalArch Biochem Biophys
Year1996
Volume336
Pages42-8
AuthorsOlsthoorn AJ, Duine JA
TitleProduction, characterization, and reconstitution of recombinant quinoprotein glucose dehydrogenase (soluble type; EC 1.1.99.17) apoenzyme of Acinetobacter calcoaceticus.
[4]
PubMed ID9342331
JournalProc Natl Acad Sci U S A
Year1997
Volume94
Pages11881-6
AuthorsZheng YJ, Bruice TC
TitleConformation of coenzyme pyrroloquinoline quinone and role of Ca2+ in the catalytic mechanism of quinoprotein methanol dehydrogenase.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
PubMed ID10508152
JournalEMBO J
Year1999
Volume18
Pages5187-94
AuthorsOubrie A, Rozeboom HJ, Kalk KH, Olsthoorn AJ, Duine JA, Dijkstra BW
TitleStructure and mechanism of soluble quinoprotein glucose dehydrogenase.
Related PDB1c9u,1cq1
Related Swiss-protP13650
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS).
PubMed ID10366508
JournalJ Mol Biol
Year1999
Volume289
Pages319-33
AuthorsOubrie A, Rozeboom HJ, Kalk KH, Duine JA, Dijkstra BW
TitleThe 1.7 A crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat.
Related PDB1qbi
Related Swiss-protP13650
[7]
CommentsX-ray crystallography
PubMed ID10518528
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages11787-91
AuthorsOubrie A, Rozeboom HJ, Dijkstra BW
TitleActive-site structure of the soluble quinoprotein glucose dehydrogenase complexed with methylhydrazine: a covalent cofactor-inhibitor complex.
Related PDB1cru
[8]
PubMed ID10924133
JournalBiochemistry
Year2000
Volume39
Pages9384-92
AuthorsDewanti AR, Duine JA
TitleCa2+-assisted, direct hydride transfer, and rate-determining tautomerization of C5-reduced PQQ to PQQH2, in the oxidation of beta-D-glucose by soluble, quinoprotein glucose dehydrogenase.
[9]
PubMed ID11761326
JournalAntioxid Redox Signal
Year2001
Volume3
Pages757-74
AuthorsAnthony C
TitlePyrroloquinoline quinone (PQQ) and quinoprotein enzymes.
[10]
PubMed ID12686124
JournalBiochim Biophys Acta
Year2003
Volume1647
Pages143-51
AuthorsOubrie A
TitleStructure and mechanism of soluble glucose dehydrogenase and other PQQ-dependent enzymes.
[11]
PubMed ID12746550
JournalMol Biotechnol
Year2003
Volume24
Pages97-104
AuthorsIgarashi S, Sode K
TitleStabilization of quaternary structure of water-soluble quinoprotein glucose dehydrogenase.
[12]
PubMed ID15234269
JournalArch Biochem Biophys
Year2004
Volume428
Pages52-63
AuthorsIgarashi S, Okuda J, Ikebukuro K, Sode K
TitleMolecular engineering of PQQGDH and its applications.
[13]
PubMed ID14982451
JournalJ Am Chem Soc
Year2004
Volume126
Pages2431-8
AuthorsReddy SY, Bruice TC
TitleMechanism of glucose oxidation by quinoprotein soluble glucose dehydrogenase: insights from molecular dynamics studies.

comments
This enzyme was transferred from E.C. 1.1.99.17 to E.C. 1.1.5.2.
This structure is "soluble" quinoprotein glucose dehydrogenase from A. calcoaceticus, which is distinct from "membrane" quinoprotein glucose dehydrogenase from A. calcoaceticus (Swiss-prot;P05465) or E.coli(Swiss-prot;P15877).
Although it binds three calcium ions per subunit, the calcium ion, which is bound to PQQ, is involved in catalysis.

createdupdated
2005-01-192009-03-17
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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