5ZZ1 | pdb_00005zz1

Probing the active center of catalase-phenol oxidase from Scytalidium thermophilum

• PDB DOI: https://doi.org/10.2210/pdb5ZZ1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycothermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-29 Released: 2019-05-29 
• Deposition Author(s): Yuzugullu Karakus, Y., Trinh, C.H., Pearson, A.R., Ogel, Z.B., McPherson, M.J.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.174 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Identification of the site of oxidase substrate binding in Scytalidium thermophilum catalase.

Yuzugullu Karakus, Y., Goc, G., Balci, S., Yorke, B.A., Trinh, C.H., McPherson, M.J., Pearson, A.R.

(2018) Acta Crystallogr D Struct Biol 74: 979-985

• PubMed: 30289408 
• DOI: https://doi.org/10.1107/S2059798318010628
• Primary Citation Related Structures: 
  5XVZ, 5XY4, 5Y17, 5ZZ1


• PubMed Abstract: 
  

  The catalase from Scytalidium thermophilum is a homotetramer containing a heme d in each active site. Although the enzyme has a classical monofunctional catalase fold, it also possesses oxidase activity towards a number of small organics, including catechol and phenol. In order to further investigate this, the crystal structure of the complex of the catalase with the classical catalase inhibitor 3-amino-1,2,4-triazole (3TR) was determined at 1.95 Å resolution. Surprisingly, no binding to the heme site was observed; instead, 3TR occupies a binding site corresponding to the NADPH-binding pocket in mammalian catalases at the entrance to a lateral channel leading to the heme. Kinetic analysis of site-directed mutants supports the assignment of this pocket as the binding site for oxidase substrates.

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Organizational Affiliation: 
• Department of Biology, Kocaeli University, Umuttepe, 41380 Kocaeli, Turkey.
The Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, 22761 Hamburg, Germany.
Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 320.53 kDa 
• Atom Count: 23,217 
• Modeled Residue Count: 2,711 
• Deposited Residue Count: 2,876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase	A, B, C, D	719	Mycothermus thermophilus	Mutation(s): 0  EC: 1.11.1.6
UniProt
Find proteins for M4GGR7 (Humicola insolens) Explore M4GGR7  Go to UniProtKB:  M4GGR7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HDD	E [auth A], J [auth B], O [auth C], S [auth D]	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE C34 H32 Fe N4 O5 UMGOPAWIGKFTRK-QQDQPIDJSA-N
3TR	F [auth A], G [auth A], K [auth B], L [auth B], N [auth B], P [auth C], Q [auth C], T [auth D]	3-AMINO-1,2,4-TRIAZOLE C2 H4 N4 KLSJWNVTNUYHDU-UHFFFAOYSA-N
CA	H [auth A], I [auth B], M [auth B], R [auth C], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.174 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.528	α = 90
b = 121.677	β = 102.16
c = 185.454	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Yuzugullu Karakus, Y., Trinh, C.H., Pearson, A.R., Ogel, Z.B., McPherson, M.J.

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Funding Organization	Location	Grant Number
Other government	Turkey	113Z744

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-07-31
  Changes: Data collection, Database references
• Version 1.2: 2019-09-11
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description