4C50

Crystal Structure of the Catalase-Peroxidase (KatG) D137S mutant from Mycobacterium Tuberculosis

PDB DOI: https://doi.org/10.2210/pdb4C50/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-09-10 Released: 2013-11-13
Deposition Author(s): Hersleth, H.-P., Zhao, X., Magliozzo, R.S., Andersson, K.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.311
R-Value Work: 0.264
R-Value Observed: 0.266

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Access Channel Residues Ser315 and Asp137 in Mycobacterium Tuberculosis Catalase-Peroxidase (Katg) Control Peroxidatic Activation of the Pro-Drug Isoniazid.

Zhao, X., Hersleth, H.P., Zhu, J., Andersson, K.K., Magliozzo, R.S.

(2013) Chem Commun (Camb) 49: 11650

PubMed: 24185282 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/c3cc47022a
Primary Citation of Related Structures:
4C50, 4C51

PubMed Abstract:
Peroxidatic activation of the anti-tuberculosis pro-drug isoniazid by Mycobacterium tuberculosis catalase-peroxidase (KatG) is regulated by gating residues of a heme access channel. The steric restriction at the bottleneck of this channel is alleviated by replacement of residue Asp137 with Ser, according to crystallographic and kinetic studies.

Organizational Affiliation

Department of Chemistry, Brooklyn College and The Graduate Center of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA. rmaglioz@brooklyn.cuny.edu.

Macromolecule Content

Total Structure Weight: 162.79 kDa
Atom Count: 11,241
Modelled Residue Count: 1,432
Deposited Residue Count: 1,480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALASE-PEROXIDASE	A, B	740	Mycobacterium tuberculosis H37Rv	Mutation(s): 1 EC: 1.11.1.21
UniProt
Find proteins for P9WIE5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIE5 Go to UniProtKB: P9WIE5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WIE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.311
R-Value Work: 0.264
R-Value Observed: 0.266
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.59	α = 90
b = 150.59	β = 90
c = 157.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-11-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-13
Type: Initial release
Version 1.1: 2013-11-27
Changes: Database references
Version 1.2: 2019-10-30
Changes: Advisory, Data collection, Derived calculations, Other
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary