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- EMDB-54872: S315T KatG mutant two Heme -

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Basic information

Entry
Database: EMDB / ID: EMD-54872
TitleS315T KatG mutant two Heme
Map data
Sample
  • Complex: KatG - Catalase peroxidase
    • Protein or peptide: Catalase-peroxidase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
KeywordsCatalase / Peoxidase / Enzyme / Heme / METAL BINDING PROTEIN
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / heme binding / metal ion binding / cytosol
Similarity search - Function
Catalase-peroxidase haem / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsChaplin AK / Allport T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci / Year: 2026
Title: Uncovering the structural impact of KatG Ser315 mutations in Mycobacterium tuberculosis via cryo-EM.
Authors: Thomas Allport / Amanda K Chaplin /
Abstract: Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is responsible for a global health burden affecting over a quarter of the world's population. The increasing prevalence of ...Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is responsible for a global health burden affecting over a quarter of the world's population. The increasing prevalence of drug-resistant TB poses a significant threat to current treatment strategies. Isoniazid (INH) is a first-line prodrug used in TB therapy, which requires activation by the catalase-peroxidase enzyme KatG. Upon activation, INH inhibits InhA, thereby disrupting mycolic acid biosynthesis, a crucial process for maintaining Mtb's distinctive, lipid-rich cell wall. The most common naturally occurring resistance-associated mutation in KatG is S315T, though other variants at this position, such as S315G, S315N, S315I, and S315R, have also been reported. In this study, we employ cryo-electron microscopy (cryo-EM) to investigate the structural basis of INH resistance conferred by these KatG variants. We present high-resolution cryo-EM structures that reveal heterogeneity in heme loading among the mutants. Detailed structural analysis highlights alterations in the hydrogen-bonding network and substrate access channel unique to each variant, offering direct comparisons with the wild-type (WT) KatG protein. Our findings provide a molecular explanation for clinical INH resistance and lay the groundwork for the rational design of next-generation anti-TB therapeutics.
History
DepositionAug 22, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54872.png

Downloads & links

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Map

FileDownload / File: emd_54872.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 288 pix.
= 237.312 Å		0.82 Å/pix.
x 288 pix.
= 237.312 Å		0.82 Å/pix.
x 288 pix.
= 237.312 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0356
Minimum - Maximum-0.074124016 - 0.21911448
Average (Standard dev.)0.00026073272 (±0.00648657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 237.312 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54872_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54872_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : KatG - Catalase peroxidase

EntireName: KatG - Catalase peroxidase
Components
  • Complex: KatG - Catalase peroxidase
    • Protein or peptide: Catalase-peroxidase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: KatG - Catalase peroxidase

SupramoleculeName: KatG - Catalase peroxidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: KatG S315G mutation
Source (natural)Organism: Mycobacterium tuberculosis (bacteria) / Location in cell: Cytoplasm
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Catalase-peroxidase

MacromoleculeName: Catalase-peroxidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: catalase-peroxidase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 84.083258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHNTSG SGGGGGRLBP RGSMSENLYF QGMPEQHPPI TETTTGAASN GCPVVGHMKY PVEGGGNQDW WPNRLNLKVL HQNPAVADP MGAAFDYAAE VATIDVDALT RDIEEVMTTS QPWWPADYGH YGPLFIRMAW HAAGTYRIHD GRGGAGGGMQ R FAPLNSWP ...String:
HHHHHHNTSG SGGGGGRLBP RGSMSENLYF QGMPEQHPPI TETTTGAASN GCPVVGHMKY PVEGGGNQDW WPNRLNLKVL HQNPAVADP MGAAFDYAAE VATIDVDALT RDIEEVMTTS QPWWPADYGH YGPLFIRMAW HAAGTYRIHD GRGGAGGGMQ R FAPLNSWP DNASLDKARR LLWPVKKKYG KKLSWADLIV FAGNCALESM GFKTFGFGFG RVDQWEPDEV YWGKEATWLG DE RYSGKRD LENPLAAVQM GLIYVNPEGP NGNPDPMAAA VDIRETFRRM AMNDVETAAL IVGGHTFGKT HGAGPADLVG PEP EAAPLE QMGLGWKSSY GTGTGKDAIT TGIEVVWTNT PTKWDNSFLE ILYGYEWELT KSPAGAWQYT AKDGAGAGTI PDPF GGPGR SPTMLATDLS LRVDPIYERI TRRWLEHPEE LADEFAKAWY KLIHRDMGPV ARYLGPLVPK QTLLWQDPVP AVSHD LVGE AEIASLKSQI RASGLTVSQL VSTAWAAASS FRGSDKRGGA NGGRIRLQPQ VGWEVNDPDG DLRKVIRTLE EIQESF NSA APGNIKVSFA DLVVLGGCAA IEKAAKAAGH NITVPFTPGR TDASQEQTDV ESFAVLEPKA DGFRNYLGKG NPLPAEY ML LDKANLLTLS APEMTVLVGG LRVLGANYKR LPLGVFTEAS ESLTNDFFVN LLDMGITWEP SPADDGTYQG KDGSGKVK W TGSRVDLVFG SNSELRALVE VYGADDAQPK FVQDFVAAWD KVMNLDRFDV R

UniProtKB: Catalase-peroxidase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
8.0 mMC32H58N2O8SCHAPSO
12.32 mMK2HPO4Potassium Phosphate dibasic
7.6778 mMKH2PO4Potassium Phosphate Monobasic

Details: 20mM Potassium phosphate 150mM Sodium Chloride 8mM CHAPSO
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2334 / Average exposure time: 2.0 sec. / Average electron dose: 49.486 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ag8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 227176
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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