Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 160.79 kDa 
• Atom Count: 12,673 
• Modelled Residue Count: 1,426 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

 5SYK

Crystal structure of B. pseudomallei KatG treated with hydrogen peroxide

• PDB DOI:  https://doi.org/10.2210/pdb5SYK/pdb
• Entry: 5SYK supersedes: 4MVP

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-11 Released: 2016-09-21 
• Deposition Author(s): Loewen, P.C.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.179 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 

Literature

An ionizable active-site tryptophan imparts catalase activity to a peroxidase core.

Loewen, P.C., Carpena, X., Vidossich, P., Fita, I., Rovira, C.

(2014) J Am Chem Soc 136: 7249-7252

• PubMed: 24785434 
• DOI: https://doi.org/10.1021/ja502794e
• Primary Citation of Related Structures:  
  5SYH, 5SYK


• PubMed Abstract: 
  

Catalase peroxidases (KatG's) are bifunctional heme proteins that can disproportionate hydrogen peroxide (catalatic reaction) despite their structural dissimilarity with monofunctional catalases. Using X-ray crystallography and QM/MM calculations, we demonstrate that the catalatic reaction of KatG's involves deprotonation of the active-site Trp, which plays a role similar to that of the distal His in monofunctional catalases. The interaction of a nearby mobile arginine with the distal Met-Tyr-Trp essential adduct (in/out) acts as an electronic switch, triggering deprotonation of the adduct Trp.

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Organizational Affiliation: 

Department of Microbiology, University of Manitoba , Winnipeg MB R3T 2N2, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase	A, B	728	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: katG, BURPS1710b_3366 EC: 1.11.1.21
UniProt
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JNW6  Go to UniProtKB:  Q3JNW6

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
MPD	L [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD	G [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
CL	E [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
OXY	F [auth A], K [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N
NA	D [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 1.80 Å
• R-Value Free: 0.179 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.72	α = 90
b = 116.2	β = 90
c = 174.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Loewen, P.C.
• This entry supersedes: 4MVP

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	D9600

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Structure summary
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence