1KDG

Crystal structure of the flavin domain of cellobiose dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Flavoprotein Domain of the Extracellular Flavocytochrome Cellobiose Dehydrogenase

Hallberg, B.M.Henriksson, G.Pettersson, G.Divne, C.

(2002) J.Mol.Biol. 315: 421-434

  • DOI: 10.1006/jmbi.2001.5246

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Department of Cell and Molecular Biology, Structural Biology, Biomedical Centre, Uppsala University, SE-751 24 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cellobiose dehydrogenase
A, B
546Phanerochaete chrysosporiumGene Names: CDH-1, CDH-2
EC: 1.1.99.18
Find proteins for Q01738 (Phanerochaete chrysosporium)
Go to UniProtKB:  Q01738
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
6FA
Query on 6FA

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A, B
6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O16 P2
BJSUUWFQAMLNKU-OKXKTURISA-N
 Ligand Interaction
UNX
Query on UNX

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B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
EMT
Query on EMT

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A
2-(ETHYLMERCURI-THIO)-BENZOIC ACID
C9 H10 Hg O2 S
HXQVQGWHFRNKMS-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

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A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
HG
Query on HG

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A, B
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.133 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 185.075α = 90.00
b = 185.075β = 90.00
c = 81.034γ = 120.00
Software Package:
Software NamePurpose
CCP4data scaling
REFMACrefinement
MLPHAREphasing
SOLVEphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2012-05-09
    Type: Structure summary