5SYH | pdb_00005syh

Structure of D141A variant of B. pseudomallei KatG

PDB DOI: https://doi.org/10.2210/pdb5SYH/pdb
Entry: 5SYH supersedes: 4KA5

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-08-11 Released: 2016-09-07
Deposition Author(s): Loewen, P.C.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.171 (Depositor), 0.180 (DCC)
R-Value Work:
0.140 (Depositor), 0.154 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/ja502794e
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 161.13 kDa
Atom Count: 12,791
Modeled Residue Count: 1,426
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase	A, B	728	Burkholderia pseudomallei 1710b	Mutation(s): 1 Gene Names: katG, BURPS1710b_3366 EC: 1.11.1.21
UniProt
Find proteins for Q939D2 (Burkholderia pseudomallei (strain K96243)) Explore Q939D2 Go to UniProtKB: Q939D2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q939D2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	G [auth A], H [auth A], N [auth B], O [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B]	I [auth A], P [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.171 (Depositor), 0.180 (DCC)
R-Value Work: 0.140 (Depositor), 0.154 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.77	α = 90
b = 113.45	β = 90
c = 174.65	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

Loewen, P.C.

This entry supersedes: 4KA5

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

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Structure summary
Version 1.2: 2018-10-10
Changes: Data collection, Database references, Structure summary
Version 1.3: 2020-01-08
Changes: Author supporting evidence, Structure summary
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection