Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 171.66 kDa 
• Atom Count: 11962 
• Modelled Residue Count: 1426 
• Deposited Residue Count: 1536 
• Unique protein chains: 1

5WHS

Crystal structure of the catalase-peroxidase from Neurospora crassa at 2.6 A

• PDB DOI: 10.2210/pdb5WHS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Neurospora crassa OR74A
• Expression System: Escherichia coli M15
• Mutation(s): No 


• Deposited: 2017-07-18 Released: 2018-01-17 
• Deposition Author(s): Diaz-Vilchis, A., Vega-Garcia, V., Rudino-Pinera, E., Hansberg, W.
• Funding Organization(s): PAPIIT-UNAM

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.254 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Literature

Structure, kinetics, molecular and redox properties of a cytosolic and developmentally regulated fungal catalase-peroxidase.

Vega-Garcia, V., Diaz-Vilchis, A., Saucedo-Vazquez, J.P., Solano-Peralta, A., Rudino-Pinera, E., Hansberg, W.

(2018) Arch Biochem Biophys 640: 17-26

• PubMed: 29305053 
• DOI: 10.1016/j.abb.2017.12.021
• Primary Citation of Related Structures:  
  5WHQ, 5WHS


• PubMed Abstract: 
  

CAT-2, a cytosolic catalase-peroxidase (CP) from Neurospora crassa, which is induced during asexual spore formation, was heterologously expressed and characterized. CAT-2 had the Met-Tyr-Trp (M-Y-W) adduct required for catalase activity. Its K _M for H ₂ O ₂ was micromolar for peroxidase and millimolar for catalase activity. A E _m  = -158 mV reduction potential value was obtained and the Soret band shift suggested a mixture of low and high spin ferric iron. CAT-2 EPR spectrum at 10 K indicated an axial and a rhombic component. With peroxyacetic acid (PAA), formation of Compound I* was observed with EPR. CAT-2 homodimer crystallographic structure contained two K ⁺ ions; Glu107 residues were displaced to bind them. CAT-2 showed the essential amino acid residues for activity in similar positions to other CPs. CAT-2 Arg426 is oriented towards the M-Y-W adduct, interacting with the deprotonated Tyr238 hydroxyl group. A perhydroxy modification of the indole nitrogen of Trp90 was oriented toward the catalytic His91. In contrast to cytochrome c peroxidase and ascorbate peroxidase, the catalase-peroxidase heme propionates are not exposed to the solvent. Together with other N. crassa enzymes that utilize H ₂ O ₂ as a substrate, CAT-2 has many tryptophan and proline residues at its surface, probably related to H ₂ O ₂ selection in water.

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Organizational Affiliation: 

Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Mexico. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase	A, B	768	Neurospora crassa OR74A	Mutation(s): 0  Gene Names: katG, cat-2, NCU05770 EC: 1.11.1.21
UniProt
Find proteins for Q8X182 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)) Explore Q8X182  Go to UniProtKB:  Q8X182

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TOX	A, B	L-PEPTIDE LINKING	C11 H12 N2 O4		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.254 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.81	α = 90
b = 142.35	β = 90
c = 183.11	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-07-18 
• Released Date: 2018-01-17 
Deposition Author(s): Diaz-Vilchis, A., Vega-Garcia, V., Rudino-Pinera, E., Hansberg, W.

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Funding Organization	Location	Grant Number
PAPIIT-UNAM	Mexico	IN208717

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references