DB code: S00165

CATH domain 2.120.10.30 : Neuraminidase Catalytic domain
E.C. 1.1.5.2
CSA 1c9u
M-CSA 1c9u
MACiE M0104

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P13650 Quinoprotein glucose dehydrogenase B
EC 1.1.5.2
Glucose dehydrogenase B [pyrroloquinoline-quinone]
Soluble glucose dehydrogenase
s-GDH
PF07995 (GSDH)
[Graphical View]

KEGG enzyme name
quinoprotein glucose dehydrogenase
D-glucose:(pyrroloquinoline-quinone) 1-oxidoreductase
glucose dehydrogenase (PQQ-dependent)
glucose dehydrogenase (pyrroloquinoline-quinone)
quinoprotein D-glucose dehydrogenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P13650 DHGB_ACICA D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol. Homodimer. Binds 1 PQQ group per subunit. Binds 3 calcium ions per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00030 Pentose phosphate pathway

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00113 C00076 C00031 C00399 C00198 C00390
E.C.
Compound PQQ Calcium D-Glucose Ubiquinone D-Glucono-1,5-lactone Ubiquinol
Type aromatic ring (with nitrogen atoms),carbohydrate,carboxyl group divalent metal (Ca2+, Mg2+) carbohydrate aromatic ring (only carbon atom),carbohydrate,lipid carbohydrate aromatic ring (only carbon atom),carbohydrate,lipid
ChEBI 18315
29108
4167
46372
16217
PubChem 1024
271
5793
5280346
7027
5280344
1c9uA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PQQ Bound:_CA_1003 Unbound Unbound Unbound Unbound
1c9uB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PQQ Bound:_CA_1003 Unbound Unbound Unbound Unbound
1cq1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PQQ Bound:_CA_503 Bound:GLC Unbound Unbound Unbound
1cq1B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PQQ Bound:_CA_503 Bound:GLC Unbound Unbound Unbound
1cruA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PQQ Bound:_CA_909 Unbound Unbound Unbound Unbound
1cruB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:PQQ-HDN Bound:_CA_908 Unbound Unbound Unbound Unbound
1qbiA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA_468 Unbound Unbound Unbound Unbound
1qbiB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA_467 Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P13650 & literature [13]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1c9uA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 144;ASP 163 GLY 247;PRO 248(Calcium binding)
1c9uB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 144;ASP 163 GLY 247;PRO 248(Calcium binding)
1cq1A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 144;ASP 163 GLY 247;PRO 248(Calcium binding)
1cq1B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 144;ASP 163 GLY 247;PRO 248(Calcium binding)
1cruA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 144;ASP 163 GLY 247;PRO 248(Calcium binding)
1cruB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 144;ASP 163 GLY 247;PRO 248(Calcium binding)
1qbiA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 144;ASP 163 GLY 247;PRO 248(Calcium binding)
1qbiB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 144;ASP 163 GLY 247;PRO 248(Calcium binding)

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 2820412
Journal Biochem Biophys Res Commun
Year 1987
Volume 147
Pages 701-9
Authors Nagasawa T, Yamada H
Title Nitrile hydratase is a quinoprotein. A possible new function of pyrroloquinoline quinone: activation of H2O in an enzymatic hydration reaction.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8411180
Journal J Mol Biol
Year 1993
Volume 233
Pages 784-6
Authors Schlunegger MP, Grutter MG, Streiff MB, Olsthoorn AJ, Duine JA
Title Crystallization and preliminary crystallographic investigations of the soluble glucose dehydrogenase from Acinetobacter calcoaceticus.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8951033
Journal Arch Biochem Biophys
Year 1996
Volume 336
Pages 42-8
Authors Olsthoorn AJ, Duine JA
Title Production, characterization, and reconstitution of recombinant quinoprotein glucose dehydrogenase (soluble type; EC 1.1.99.17) apoenzyme of Acinetobacter calcoaceticus.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9342331
Journal Proc Natl Acad Sci U S A
Year 1997
Volume 94
Pages 11881-6
Authors Zheng YJ, Bruice TC
Title Conformation of coenzyme pyrroloquinoline quinone and role of Ca2+ in the catalytic mechanism of quinoprotein methanol dehydrogenase.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID
PubMed ID 10508152
Journal EMBO J
Year 1999
Volume 18
Pages 5187-94
Authors Oubrie A, Rozeboom HJ, Kalk KH, Olsthoorn AJ, Duine JA, Dijkstra BW
Title Structure and mechanism of soluble quinoprotein glucose dehydrogenase.
Related PDB 1c9u 1cq1
Related UniProtKB P13650
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS).
Medline ID
PubMed ID 10366508
Journal J Mol Biol
Year 1999
Volume 289
Pages 319-33
Authors Oubrie A, Rozeboom HJ, Kalk KH, Duine JA, Dijkstra BW
Title The 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 PDB 1qbi
Related UniProtKB P13650
[7]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10518528
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 11787-91
Authors Oubrie A, Rozeboom HJ, Dijkstra BW
Title Active-site structure of the soluble quinoprotein glucose dehydrogenase complexed with methylhydrazine: a covalent cofactor-inhibitor complex.
Related PDB 1cru
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10924133
Journal Biochemistry
Year 2000
Volume 39
Pages 9384-92
Authors Dewanti AR, Duine JA
Title Ca2+-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.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11761326
Journal Antioxid Redox Signal
Year 2001
Volume 3
Pages 757-74
Authors Anthony C
Title Pyrroloquinoline quinone (PQQ) and quinoprotein enzymes.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 12686124
Journal Biochim Biophys Acta
Year 2003
Volume 1647
Pages 143-51
Authors Oubrie A
Title Structure and mechanism of soluble glucose dehydrogenase and other PQQ-dependent enzymes.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 12746550
Journal Mol Biotechnol
Year 2003
Volume 24
Pages 97-104
Authors Igarashi S, Sode K
Title Stabilization of quaternary structure of water-soluble quinoprotein glucose dehydrogenase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 15234269
Journal Arch Biochem Biophys
Year 2004
Volume 428
Pages 52-63
Authors Igarashi S, Okuda J, Ikebukuro K, Sode K
Title Molecular engineering of PQQGDH and its applications.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 14982451
Journal J Am Chem Soc
Year 2004
Volume 126
Pages 2431-8
Authors Reddy SY, Bruice TC
Title Mechanism of glucose oxidation by quinoprotein soluble glucose dehydrogenase: insights from molecular dynamics studies.
Related PDB
Related UniProtKB

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.

Created Updated
2005-01-19 2009-03-17