4QI7

Cellobiose dehydrogenase from Neurospora crassa, NcCDH

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.

Tan, T.C., Kracher, D., Gandini, R., Sygmund, C., Kittl, R., Haltrich, D., Hallberg, B.M., Ludwig, R., Divne, C.

(2015) Nat Commun 6: 7542-7542

  • DOI: https://doi.org/10.1038/ncomms8542
  • Primary Citation of Related Structures:  
    4QI3, 4QI4, 4QI5, 4QI6, 4QI7, 4QI8

  • PubMed Abstract: 

    • A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH ...

    A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH. CDH contains a haem-binding cytochrome (CYT) connected via a flexible linker to a flavin-dependent dehydrogenase (DH). Electrons are generated from cellobiose oxidation catalysed by DH and shuttled via CYT to LPMO. Here we present structural analyses that provide a comprehensive picture of CDH conformers, which govern the electron transfer between redox centres. Using structure-based site-directed mutagenesis, rapid kinetics analysis and molecular docking, we demonstrate that flavin-to-haem interdomain electron transfer (IET) is enabled by a haem propionate group and that rapid IET requires a closed CDH state in which the propionate is tightly enfolded by DH. Following haem reduction, CYT reduces LPMO to initiate oxygen activation at the copper centre and subsequent cellulose depolymerization.

    Organizational Affiliation: 

    1] School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden [2] Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cellobiose dehydrogenase
A, B
806Neurospora crassa OR74AMutation(s): 0 
Gene Names: cdh-1, NCU00206
UniProt
Find proteins for Q7RXM0 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore Q7RXM0 
Go to UniProtKB:  Q7RXM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7RXM0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
D [auth A],
DA [auth B]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
HEM
Query on HEM
Download Ideal Coordinates CCD File 
C [auth A],
CA [auth B]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
E [auth A]
EA [auth B]
F [auth A]
FA [auth B]
G [auth A]
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
PT
Query on PT
Download Ideal Coordinates CCD File 
MA [auth B]
N [auth A]
NA [auth B]
O [auth A]
OA [auth B]
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N		 Ligand Interaction
MAN
Query on MAN
Download Ideal Coordinates CCD File 
KA [auth B],
L [auth A],
LA [auth B],
M [auth A]		alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
UA [auth B],
Z [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.599α = 90
b = 141.851β = 90
c = 146.998γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Polymer sequence, Structure summary