spacer
spacer

PDBsum entry 1naa

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1naa
Jmol
Contents
Protein chains
541 a.a. *
Ligands
NAG ×5
6FA ×2
ABL ×2
Waters ×1007
* Residue conservation analysis
PDB id:
1naa
Name: Oxidoreductase
Title: Cellobiose dehydrogenase flavoprotein fragment in complex wi cellobionolactam
Structure: Cellobiose dehydrogenase. Chain: a, b. Fragment: c-terminal flavoprotein fragment. Synonym: cdh, cellobiose-quinone oxidoreductase. Ec: 1.1.99.18
Source: Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: k3
Resolution:
1.80Å     R-factor:   0.146     R-free:   0.185
Authors: B.M.Hallberg,G.Henriksson,G.Pettersson,A.Vasella,C.Divne
Key ref:
B.M.Hallberg et al. (2003). Mechanism of the reductive half-reaction in cellobiose dehydrogenase. J Biol Chem, 278, 7160-7166. PubMed id: 12493734 DOI: 10.1074/jbc.M210961200
Date:
27-Nov-02     Release date:   14-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q01738  (CDH_PHACH) -  Cellobiose dehydrogenase
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: Cellobiose + acceptor = cellobiono-1,5-lactone + reduced acceptor
Cellobiose
Bound ligand (Het Group name = ABL)
matches with 91.67% similarity
+ 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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity, acting on CH-OH group of donors     2 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M210961200 J Biol Chem 278:7160-7166 (2003)
PubMed id: 12493734  
 
 
Mechanism of the reductive half-reaction in cellobiose dehydrogenase.
B.M.Hallberg, G.Henriksson, G.Pettersson, A.Vasella, C.Divne.
 
  ABSTRACT  
 
The extracellular flavocytochrome cellobiose dehydrogenase (CDH; EC ) participates in lignocellulose degradation by white-rot fungi with a proposed role in the early events of wood degradation. The complete hemoflavoenzyme consists of a catalytically active dehydrogenase fragment (DH(cdh)) connected to a b-type cytochrome domain via a linker peptide. In the reductive half-reaction, DH(cdh) catalyzes the oxidation of cellobiose to yield cellobiono-1,5-lactone. The active site of DH(cdh) is structurally similar to that of glucose oxidase and cholesterol oxidase, with a conserved histidine residue positioned at the re face of the flavin ring close to the N5 atom. The mechanisms of oxidation in glucose oxidase and cholesterol oxidase are still poorly understood, partly because of lack of experimental structure data or difficulties in interpreting existing data for enzyme-ligand complexes. Here we report the crystal structure of the Phanerochaete chrysosporium DH(cdh) with a bound inhibitor, cellobiono-1,5-lactam, at 1.8-A resolution. The distance between the lactam C1 and the flavin N5 is only 2.9 A, implying that in an approximately planar transition state, the maximum distance for the axial 1-hydrogen to travel for covalent addition to N5 is 0.8-0.9 A. The lactam O1 interacts intimately with the side chains of His-689 and Asn-732. Our data lend substantial structural support to a reaction mechanism where His-689 acts as a general base by abstracting the O1 hydroxyl proton in concert with transfer of the C1 hydrogen as hydride to the re face of the flavin N5.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Molecules discussed in the text. a, cellobiose; b, cellobionolactone; c, cellobionolactam.
Figure 2.
Fig. 2. Structure of the DH [cdh] with bound cellobionolactam. a, overall structure of the DH[cdh] fragment with bound cellobionolactam in the active site. The polypeptide chain has been color ramped from the N terminus (blue) to the C terminus (red). helices and strands are shown as spirals and arrows, respectively. The FAD cofactor and the ligand are shown as ball-and-stick representations. Atom colors are blue for nitrogen, red for oxygen, and for carbon, yellow (FAD) or green (Cblm). The schematic was made with the program PyMOL, www.pymol.org (40). b, [A]-weighted F[o] F[c] electron density map calculated to 2.0-Å resolution using the model from the first simulated-annealing refinement with CNS where only protein atoms had been included and refined. The electron density for the ligand is, therefore, free from model bias.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 7160-7166) copyright 2003.  
  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.  
20467737 D.Ribitsch, S.Winkler, K.Gruber, W.Karl, E.Wehrschütz-Sigl, I.Eiteljörg, P.Schratl, P.Remler, R.Stehr, C.Bessler, N.Mussmann, K.Sauter, K.H.Maurer, and H.Schwab (2010).
Engineering of choline oxidase from Arthrobacter nicotianae for potential use as biological bleach in detergents.
  Appl Microbiol Biotechnol, 87, 1743-1752.  
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
19256550 I.Dreveny, A.S.Andryushkova, A.Glieder, K.Gruber, and C.Kratky (2009).
Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity.
  Biochemistry, 48, 3370-3377.
PDB codes: 3gdn 3gdp
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.  
16332885 M.H.Lee, W.L.Lai, S.F.Lin, C.S.Hsu, S.H.Liaw, and Y.C.Tsai (2005).
Structural characterization of glucooligosaccharide oxidase from Acremonium strictum.
  Appl Environ Microbiol, 71, 8881-8887.  
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.