Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43084.02 
• Atom Count: 3005 
• Residue Count: 372 
• Unique protein chains: 1

1PL3

Cytochrome Domain Of Cellobiose Dehydrogenase, M65H mutant

• DOI: 10.2210/pdb1PL3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Phanerochaete chrysosporium
• Expression System: Phanerochaete chrysosporium
• Mutation(s): 1 


• Deposited: 2003-06-06 Released: 2003-07-01 
• Deposition Author(s): Rotsaert, F.A.J., Hallberg, B.M., de Vries, S., Moenne-Loccoz, P., Divne, C., Gold, M.H.

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Experimental Data Snapshot

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

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

• PubMed: 12796496 
• 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-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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Cellobiose dehydrogenase	A, B	186	Phanerochaete chrysosporium	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
1PG	A	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CD	A, B	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

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 = 139.033	α = 90.00
b = 139.033	β = 90.00
c = 52.668	γ = 120.00

Software Package:

Software Name	Purpose
SCALA	data scaling
CCP4	data scaling
MOSFLM	data reduction
CNS	phasing
CNS	refinement
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-06 
• Released Date: 2003-07-01 
• Deposition Author(s): Rotsaert, F.A.J., Hallberg, B.M., de Vries, S., Moenne-Loccoz, P., Divne, C., Gold, M.H.

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