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PDBsum entry 1kdg
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1kdg

 

 

 

 

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Contents
Protein chains
541 a.a. *
Ligands
NAG ×5
MAN ×4
6FA ×2
EMT
UNX
Metals
_HG ×9
Waters ×1120
* Residue conservation analysis
PDB id:
1kdg
Name: Oxidoreductase
Title: Crystal structure of the flavin domain of cellobiose dehydrogenase
Structure: Cellobiose dehydrogenase. Chain: a, b. Fragment: c-terminal flavoprotein domain. Synonym: cdh. Cellobiose-quinone oxidoreductase. Ec: 1.1.99.18
Source: Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: k3. Other_details: secreted
Resolution:
1.50Å     R-factor:   0.135     R-free:   0.169
Authors: B.M.Hallberg,G.Henriksson,G.Pettersson,C.Divne
Key ref:
B.M.Hallberg et al. (2002). Crystal structure of the flavoprotein domain of the extracellular flavocytochrome cellobiose dehydrogenase. J Mol Biol, 315, 421-434. PubMed id: 11786022 DOI: 10.1006/jmbi.2001.5246
Date:
13-Nov-01     Release date:   13-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q01738  (CDH_PHACH) -  Cellobiose dehydrogenase from Phanerodontia chrysosporium
Seq:
Struc: 		 
Seq:
Struc: 		773 a.a.
541 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.99.18  - cellobiose dehydrogenase (acceptor).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-cellobiose + A = D-cellobiono-1,5-lactone + AH2
Cellobiose
 + acceptor
 = cellobiono-1,5-lactone
 + reduced acceptor
      Cofactor: FAD; Heme
FAD
Bound ligand (Het Group name = 6FA) matches with 98.15% similarity 		Heme
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2001.5246 J Mol Biol 315:421-434 (2002)
PubMed id: 11786022  
 
 
Crystal structure of the flavoprotein domain of the extracellular flavocytochrome cellobiose dehydrogenase.
B.M.Hallberg, G.Henriksson, G.Pettersson, C.Divne.
 
  ABSTRACT  
 
Cellobiose dehydrogenase (CDH) participates in the degradation of cellulose and lignin. The protein is an extracellular flavocytochrome with a b-type cytochrome domain (CYT(cdh)) connected to a flavodehydrogenase domain (DH(cdh)). DH(cdh) catalyses a two-electron oxidation at the anomeric C1 position of cellobiose to yield cellobiono-1,5-lactone, and the electrons are subsequently transferred from DH(cdh) to an acceptor, either directly or via CYT(cdh). Here, we describe the crystal structure of Phanerochaete chrysosporium DH(cdh) determined at 1.5 A resolution. DH(cdh) belongs to the GMC family of oxidoreductases, which includes glucose oxidase (GOX) and cholesterol oxidase (COX); however, the sequence identity with members of the family is low. The overall fold of DH(cdh) is p-hydroxybenzoate hydroxylase-like and is similar to, but also different from, that of GOX and COX. It is partitioned into an FAD-binding subdomain of alpha/beta type and a substrate-binding subdomain consisting of a seven-stranded beta sheet and six helices. Docking of CYT(cdh) and DH(cdh) suggests that CYT(cdh) covers the active-site entrance in DH(cdh), and that the resulting distance between the cofactors is within acceptable limits for inter-domain electron transfer. Based on docking of the substrate, cellobiose, in the active site of DH(cdh), we propose that the enzyme discriminates against glucose by favouring interaction with the non-reducing end of cellobiose.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Comparison of the loop-and-lid structure in COX, GOX and DH[cdh]. (a) COX[Bre] (loop 46-94; lid 95-109), (b) GOX[Asp] (loop 54-75; lid 76-97), and (c) DH[cdh] (loop 250-288; lid residues 289-299). The loop and lid segments are coloured red and blue, respectively. The flavin cofactor is coloured yellow. The picture was made as described for Figure 1(a). 		Figure 7.
Figure 7. Stereo view of the superimposed active sites in DH[cdh], GOX and COX. Atom colours: carbon (DH[cdh], yellow; GOX, pink; COX, green); oxygen, red; nitrogen, blue. Residues Asn309, His689 and Asn732, as well as the isoalloxazine ring of the FAD cofactor are shown for DH[cdh]. Superposition was made to obtain optimal alignment of the pyrimidine moiety and the N5 atom of the flavin ring system. The picture was made as described for Figure 1(a).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 315, 421-434) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21381206 L.G.Vasilchenko, K.N.Karapetyan, O.P.Yershevich, R.Ludwig, M.Zamocky, C.K.Peterbauer, D.Haltrich, and M.L.Rabinovich (2011).
Cellobiose dehydrogenase of Chaetomium sp. INBI 2-26(-): Structural basis of enhanced activity toward glucose at neutral pH.
  Biotechnol J, 6, 538-553.  
20709172 R.Zhang, Z.Fan, and T.Kasuga (2011).
Expression of cellobiose dehydrogenase from Neurospora crassa in Pichia pastoris and its purification and characterization.
  Protein Expr Purif, 75, 63-69.  
20140751 Desriani, S.Ferri, and K.Sode (2010).
Functional expression of Phanerochaete chrysosporium cellobiose dehydrogenase flavin domain in Escherichia coli.
  Biotechnol Lett, 32, 855-859.  
20528921 O.Spadiut, T.C.Tan, I.Pisanelli, D.Haltrich, and C.Divne (2010).
Importance of the gating segment in the substrate-recognition loop of pyranose 2-oxidase.
  FEBS J, 277, 2892-2909.
PDB codes: 3k4j 3k4k 3k4l 3k4m 3k4n
20661990 R.Ludwig, W.Harreither, F.Tasca, and L.Gorton (2010).
Cellobiose dehydrogenase: a versatile catalyst for electrochemical applications.
  Chemphyschem, 11, 2674-2697.  
19923715 I.S.Fernández, F.J.Ruíz-Dueñas, E.Santillana, P.Ferreira, M.J.Martínez, A.T.Martínez, and A.Romero (2009).
Novel structural features in the GMC family of oxidoreductases revealed by the crystal structure of fungal aryl-alcohol oxidase.
  Acta Crystallogr D Biol Crystallogr, 65, 1196-1205.
PDB code: 3fim
19574215 P.Ferreira, A.Hernandez-Ortega, B.Herguedas, A.T.Martínez, and M.Medina (2009).
Aryl-alcohol oxidase involved in lignin degradation: a mechanistic study based on steady and pre-steady state kinetics and primary and solvent isotope effects with two alcohol substrates.
  J Biol Chem, 284, 24840-24847.  
19270118 W.Harreither, C.Sygmund, E.Dünhofen, R.Vicuña, D.Haltrich, and R.Ludwig (2009).
Cellobiose dehydrogenase from the ligninolytic basidiomycete Ceriporiopsis subvermispora.
  Appl Environ Microbiol, 75, 2750-2757.  
18482980 C.Michalski, H.Mohagheghi, M.Nimtz, J.Pasteels, and D.Ober (2008).
Salicyl alcohol oxidase of the chemical defense secretion of two chrysomelid leaf beetles. Molecular and functional characterization of two new members of the glucose-methanol-choline oxidoreductase gene family.
  J Biol Chem, 283, 19219-19228.  
18371173 P.Baldrian, and V.Valásková (2008).
Degradation of cellulose by basidiomycetous fungi.
  FEMS Microbiol Rev, 32, 501-521.  
17227387 M.Kujawa, J.Volc, P.Halada, P.Sedmera, C.Divne, C.Sygmund, C.Leitner, C.Peterbauer, and D.Haltrich (2007).
Properties of pyranose dehydrogenase purified from the litter-degrading fungus Agaricus xanthoderma.
  FEBS J, 274, 879-894.  
16984920 M.Kujawa, H.Ebner, C.Leitner, B.M.Hallberg, M.Prongjit, J.Sucharitakul, R.Ludwig, U.Rudsander, C.Peterbauer, P.Chaiyen, D.Haltrich, and C.Divne (2006).
Structural basis for substrate binding and regioselective oxidation of monosaccharides at C3 by pyranose 2-oxidase.
  J Biol Chem, 281, 35104-35115.
PDB codes: 2igk 2igm 2ign 2igo
16999821 P.Ferreira, F.J.Ruiz-Dueñas, M.J.Martínez, W.J.van Berkel, and A.T.Martínez (2006).
Site-directed mutagenesis of selected residues at the active site of aryl-alcohol oxidase, an H2O2-producing ligninolytic enzyme.
  FEBS J, 273, 4878-4888.  
15958387 K.R.Marshall, M.Gong, L.Wodke, J.H.Lamb, D.J.Jones, P.B.Farmer, N.S.Scrutton, and A.W.Munro (2005).
The human apoptosis-inducing protein AMID is an oxidoreductase with a modified flavin cofactor and DNA binding activity.
  J Biol Chem, 280, 30735-30740.  
15741070 L.Stoica, N.Dimcheva, D.Haltrich, T.Ruzgas, and L.Gorton (2005).
Electrochemical investigation of cellobiose dehydrogenase from new fungal sources on Au electrodes.
  Biosens Bioelectron, 20, 2010-2018.  
  16233666 T.Kajisa, M.Yoshida, K.Igarashi, A.Katayama, T.Nishino, and M.Samejima (2004).
Characterization and molecular cloning of cellobiose dehydrogenase from the brown-rot fungus Coniophora puteana.
  J Biosci Bioeng, 98, 57-63.  
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
14690428 M.Ghanem, F.Fan, K.Francis, and G.Gadda (2003).
Spectroscopic and kinetic properties of recombinant choline oxidase from Arthrobacter globiformis.
  Biochemistry, 42, 15179-15188.  
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.

 

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