1PL3

Cytochrome Domain Of Cellobiose Dehydrogenase, M65H mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Biophysical and Structural Analysis of a Novel Heme b Iron Ligation in the Flavocytochrome Cellobiose Dehydrogenase.

Rotsaert, F.A.J.Hallberg, B.M.De Vries, S.Moenne-Loccoz, P.Divne, C.Renganathan, V.Gold, M.H.

(2003) J.Biol.Chem. 278: 33224-33231

  • DOI: 10.1074/jbc.M302653200

  • PubMed Abstract: 
  • The fungal extracellular flavocytochrome cellobiose dehydrogenase (CDH) participates in lignocellulose degradation. The enzyme has a cytochrome domain connected to a flavin-binding domain by a peptide linker. The cytochrome domain contains a 6-coordi ...

    The fungal extracellular flavocytochrome cellobiose dehydrogenase (CDH) participates in lignocellulose degradation. The enzyme has a cytochrome domain connected to a flavin-binding domain by a peptide linker. The cytochrome domain contains a 6-coordinate low spin b-type heme with unusual iron ligands and coordination geometry. Wild type CDH is only the second example of a b-type heme with Met-His ligation, and it is the first example of a Met-His ligation of heme b where the ligands are arranged in a nearly perpendicular orientation. To investigate the ligation further, Met65 was replaced with a histidine to create a bis-histidyl ligated iron typical of b-type cytochromes. The variant is expressed as a stable 90-kDa protein that retains the flavin domain catalytic reactivity. However, the ability of the mutant to reduce external one-electron acceptors such as cytochrome c is impaired. Electrochemical measurements demonstrate a decrease in the redox midpoint potential of the heme by 210 mV. In contrast to the wild type enzyme, the ferric state of the protoheme displays a mixed low spin/high spin state at room temperature and low spin character at 90 K, as determined by resonance Raman spectroscopy. The wild type cytochrome does not bind CO, but the ferrous state of the variant forms a CO complex, although the association rate is very low. The crystal structure of the M65H cytochrome domain has been determined at 1.9 A resolution. The variant structure confirms a bis-histidyl ligation but reveals unusual features. As for the wild type enzyme, the ligands have a nearly perpendicular arrangement. Furthermore, the iron is bound by imidazole N delta 1 and N epsilon 2 nitrogen atoms, rather than the typical N epsilon 2/N epsilon 2 coordination encountered in bis-histidyl ligated heme proteins. To our knowledge, this is the first example of a bis-histidyl N delta 1/N epsilon 2-coordinated protoporphyrin IX iron.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, OGI School of Science and Engineering at Oregon Health & Science University, Beaverton, Oregon 97006-8921, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellobiose dehydrogenase
A, B
186Phanerochaete chrysosporiumMutation(s): 1 
Gene Names: CDH-1, CDH-2
EC: 1.1.99.18
Find proteins for Q01738 (Phanerochaete chrysosporium)
Go to UniProtKB:  Q01738
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PG
Query on 1PG

Download SDF File 
Download CCD File 
A
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-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: 1.9 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 139.033α = 90.00
b = 139.033β = 90.00
c = 52.668γ = 120.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement
CNSrefinement
CNSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description