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PDBsum entry 1c9u

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1c9u
Jmol
Contents
Protein chains
444 a.a. *
Ligands
PQQ ×2
GOL ×4
Metals
_CA ×6
Waters ×548
* Residue conservation analysis
PDB id:
1c9u
Name: Oxidoreductase
Title: Crystal structure of the soluble quinoprotein glucose dehydr complex with pqq
Structure: Soluble quinoprotein glucose dehydrogenase. Chain: a, b. Engineered: yes
Source: Acinetobacter calcoaceticus. Organism_taxid: 471. Cellular_location: periplasm. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.224     R-free:   0.286
Authors: A.Oubrie,H.J.Rozeboom,B.W.Dijkstra
Key ref:
A.Oubrie et al. (1999). Structure and mechanism of soluble quinoprotein glucose dehydrogenase. EMBO J, 18, 5187-5194. PubMed id: 10508152 DOI: 10.1093/emboj/18.19.5187
Date:
03-Aug-99     Release date:   04-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P13650  (DHGB_ACICA) -  Quinoprotein glucose dehydrogenase B
Seq:
Struc:
478 a.a.
444 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.5.2  - Quinoprotein glucose dehydrogenase (PQQ, quinone).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol
D-glucose
Bound ligand (Het Group name = GOL)
matches with 50.00% similarity
+ ubiquinone
= D-glucono-1,5-lactone
+ ubiquinol
      Cofactor: Ca(2+) or Mg(2+); Pyrroloquinoline quinone
Ca(2+)
or Mg(2+)
Pyrroloquinoline quinone
Bound ligand (Het Group name = PQQ) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1093/emboj/18.19.5187 EMBO J 18:5187-5194 (1999)
PubMed id: 10508152  
 
 
Structure and mechanism of soluble quinoprotein glucose dehydrogenase.
A.Oubrie, H.J.Rozeboom, K.H.Kalk, A.J.Olsthoorn, J.A.Duine, B.W.Dijkstra.
 
  ABSTRACT  
 
Soluble glucose dehydrogenase (s-GDH; EC 1.1.99.17) is a classical quinoprotein which requires the cofactor pyrroloquinoline quinone (PQQ) to oxidize glucose to gluconolactone. The reaction mechanism of PQQ-dependent enzymes has remained controversial due to the absence of comprehensive structural data. We have determined the X-ray structure of s-GDH with the cofactor at 2.2 A resolution, and of a complex with reduced PQQ and glucose at 1.9 A resolution. These structures reveal the active site of s-GDH, and show for the first time how a functionally bound substrate interacts with the cofactor in a PQQ-dependent enzyme. Twenty years after the discovery of PQQ, our results finally provide conclusive evidence for a reaction mechanism comprising general base-catalyzed hydride transfer, rather than the generally accepted covalent addition-elimination mechanism. Thus, PQQ-dependent enzymes use a mechanism similar to that of nicotinamide- and flavin-dependent oxidoreductases.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Ribbon diagram of the overall structure of the dimer of s-GDH from A.calcoaceticus. The two monomers are shown in blue and green. Calcium ions are shown as yellow spheres. PQQ is shown in ball-and-stick representation. This picture was produced with MOLSCRIPT (Kraulis, 1991).
Figure 5.
Figure 5 Representative view of the binding of PQQH[2] and glucose to s-GDH. Surface drawing of s-GDH created using the program GRASP (Nicholls et al., 1991). PQQH[2] and glucose are shown in ball-and-stick representation.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 5187-5194) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21356200 J.Li, J.H.Gan, F.S.Mathews, and Z.X.Xia (2011).
The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase.
  Biochem Biophys Res Commun, 406, 621-626.
PDB codes: 2ad6 2ad7 2ad8
20936374 L.Tetianec, I.Bratkovskaja, J.Kulys, V.Casaite, and R.Meskys (2011).
Probing Reactivity of PQQ-Dependent Carbohydrate Dehydrogenases Using Artificial Electron Acceptor.
  Appl Biochem Biotechnol, 163, 404-414.  
20886312 M.Hofer, K.Bönsch, T.Greiner-Stöffele, and M.Ballschmiter (2011).
Characterization and Engineering of a Novel Pyrroloquinoline Quinone Dependent Glucose Dehydrogenase from Sorangium cellulosum So ce56.
  Mol Biotechnol, 47, 253-261.  
20669254 J.Kulys, L.Tetianec, and I.Bratkovskaja (2010).
Pyrroloquinoline quinone-dependent carbohydrate dehydrogenase: activity enhancement and the role of artificial electron acceptors.
  Biotechnol J, 5, 822-828.  
19598234 S.W.Fan, R.A.George, N.L.Haworth, L.L.Feng, J.Y.Liu, and M.A.Wouters (2009).
Conformational changes in redox pairs of protein structures.
  Protein Sci, 18, 1745-1765.  
17291745 C.Lau, S.Borgmann, M.Maciejewska, B.Ngounou, P.Gründler, and W.Schuhmann (2007).
Improved specificity of reagentless amperometric PQQ-sGDH glucose biosensors by using indirectly heated electrodes.
  Biosens Bioelectron, 22, 3014-3020.  
16567634 C.W.Kay, B.Mennenga, H.Görisch, and R.Bittl (2006).
Substrate binding in quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa studied by electron-nuclear double resonance.
  Proc Natl Acad Sci U S A, 103, 5267-5272.  
16267040 C.W.Kay, B.Mennenga, H.Görisch, and R.Bittl (2006).
Structure of the pyrroloquinoline quinone radical in quinoprotein ethanol dehydrogenase.
  J Biol Chem, 281, 1470-1476.  
16944137 N.Hamamatsu, A.Suzumura, Y.Nomiya, M.Sato, T.Aita, M.Nakajima, Y.Husimi, and Y.Shibanaka (2006).
Modified substrate specificity of pyrroloquinoline quinone glucose dehydrogenase by biased mutation assembling with optimized amino acid substitution.
  Appl Microbiol Biotechnol, 73, 607-617.  
16864586 S.M.Southall, J.J.Doel, D.J.Richardson, and A.Oubrie (2006).
Soluble aldose sugar dehydrogenase from Escherichia coli: a highly exposed active site conferring broad substrate specificity.
  J Biol Chem, 281, 30650-30659.
PDB code: 2g8s
15590279 C.Zhao, and G.Wittstock (2005).
Scanning electrochemical microscopy for detection of biosensor and biochip surfaces with immobilized pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase as enzyme label.
  Biosens Bioelectron, 20, 1277-1284.  
15715904 S.Tanaka, S.Igarashi, S.Ferri, and K.Sode (2005).
Increasing stability of water-soluble PQQ glucose dehydrogenase by increasing hydrophobic interaction at dimeric interface.
  BMC Biochem, 6, 1.  
15480576 A.C.Schwartz, G.Gockel, J.Gross, B.Moritz, and H.E.Meyer (2004).
Relations and functions of dye-linked formaldehyde dehydrogenase from Hyphomicrobium zavarzinii revealed by sequence determination and analysis.
  Arch Microbiol, 182, 458-466.  
14612441 M.D.Elias, S.Nakamura, C.T.Migita, H.Miyoshi, H.Toyama, K.Matsushita, O.Adachi, and M.Yamada (2004).
Occurrence of a bound ubiquinone and its function in Escherichia coli membrane-bound quinoprotein glucose dehydrogenase.
  J Biol Chem, 279, 3078-3083.  
15148379 O.T.Magnusson, H.Toyama, M.Saeki, A.Rojas, J.C.Reed, R.C.Liddington, J.P.Klinman, and R.Schwarzenbacher (2004).
Quinone biogenesis: Structure and mechanism of PqqC, the final catalyst in the production of pyrroloquinoline quinone.
  Proc Natl Acad Sci U S A, 101, 7913-7918.
PDB codes: 1otv 1otw
15273299 S.Y.Reddy, and T.C.Bruice (2004).
Determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase.
  Protein Sci, 13, 1965-1978.  
15520392 S.Y.Reddy, and T.C.Bruice (2004).
Mechanisms of ammonia activation and ammonium ion inhibition of quinoprotein methanol dehydrogenase: a computational approach.
  Proc Natl Acad Sci U S A, 101, 15887-15892.  
12493734 B.M.Hallberg, G.Henriksson, G.Pettersson, A.Vasella, and C.Divne (2003).
Mechanism of the reductive half-reaction in cellobiose dehydrogenase.
  J Biol Chem, 278, 7160-7166.
PDB code: 1naa
11714714 A.Oubrie, H.J.Rozeboom, K.H.Kalk, E.G.Huizinga, and B.W.Dijkstra (2002).
Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni: structural basis for substrate oxidation and electron transfer.
  J Biol Chem, 277, 3727-3732.
PDB code: 1kb0
11889098 A.S.Vangnai, D.J.Arp, and L.A.Sayavedra-Soto (2002).
Two distinct alcohol dehydrogenases participate in butane metabolism by Pseudomonas butanovora.
  J Bacteriol, 184, 1916-1924.  
12057198 Z.W.Chen, K.Matsushita, T.Yamashita, T.A.Fujii, H.Toyama, O.Adachi, H.D.Bellamy, and F.S.Mathews (2002).
Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5.
  Structure, 10, 837-849.
PDB code: 1kv9
12116408 A.Jongejan, J.A.Jongejan, and W.R.Hagen (2001).
Direct hydride transfer in the reaction mechanism of quinoprotein alcohol dehydrogenases: a quantum mechanical investigation.
  J Comput Chem, 22, 1732-1749.  
11761326 C.Anthony (2001).
Pyrroloquinoline quinone (PQQ) and quinoprotein enzymes.
  Antioxid Redox Signal, 3, 757-774.  
11149955 Y.J.Zheng, Xia Zx, Chen Zw, F.S.Mathews, and T.C.Bruice (2001).
Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation.
  Proc Natl Acad Sci U S A, 98, 432-434.
PDB code: 1g72
  10933491 A.Oubrie, and B.W.Dijkstra (2000).
Structural requirements of pyrroloquinoline quinone dependent enzymatic reactions.
  Protein Sci, 9, 1265-1273.  
10924133 A.R.Dewanti, and J.A.Duine (2000).
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.
  Biochemistry, 39, 9384-9392.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.