+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11234 | |||||||||
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Title | Cryo-EM structure of wild-type KatG from M. tuberculosis | |||||||||
Map data | WT KatG | |||||||||
Sample |
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Keywords | Heme / Peroxidase-Catalase / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Blundell TL / Chaplin AK | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Structure / Year: 2021 Title: Using cryo-EM to understand antimycobacterial resistance in the catalase-peroxidase (KatG) from Mycobacterium tuberculosis. Authors: Asma Munir / Michael T Wilson / Steven W Hardwick / Dimitri Y Chirgadze / Jonathan A R Worrall / Tom L Blundell / Amanda K Chaplin / Abstract: Resolution advances in cryoelectron microscopy (cryo-EM) now offer the possibility to visualize structural effects of naturally occurring resistance mutations in proteins and also of understanding ...Resolution advances in cryoelectron microscopy (cryo-EM) now offer the possibility to visualize structural effects of naturally occurring resistance mutations in proteins and also of understanding the binding mechanisms of small drug molecules. In Mycobacterium tuberculosis the multifunctional heme enzyme KatG is indispensable for activation of isoniazid (INH), a first-line pro-drug for treatment of tuberculosis. We present a cryo-EM methodology for structural and functional characterization of KatG and INH resistance variants. The cryo-EM structure of the 161 kDa KatG dimer in the presence of INH is reported to 2.7 Å resolution allowing the observation of potential INH binding sites. In addition, cryo-EM structures of two INH resistance variants, identified from clinical isolates, W107R and T275P, are reported. In combination with electronic absorbance spectroscopy our cryo-EM approach reveals how these resistance variants cause disorder in the heme environment preventing heme uptake and retention, providing insight into INH resistance. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11234.map.gz | 167.9 MB | EMDB map data format | |
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Header (meta data) | emd-11234-v30.xml emd-11234.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11234_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_11234.png | 14.3 KB | ||
Filedesc metadata | emd-11234.cif.gz | 5.7 KB | ||
Others | emd_11234_half_map_1.map.gz emd_11234_half_map_2.map.gz | 165.3 MB 165.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11234 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11234 | HTTPS FTP |
-Related structure data
Related structure data | 6zjiMC 7a2iC 7a7aC 7a7cC 7a8zC 7aa3C 7ag8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11234.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | WT KatG | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: WT KatG half map A
File | emd_11234_half_map_1.map | ||||||||||||
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Annotation | WT KatG half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: WT KatG half map B
File | emd_11234_half_map_2.map | ||||||||||||
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Annotation | WT KatG half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of WT KatG from M. tuberculosis
Entire | Name: Cryo-EM structure of WT KatG from M. tuberculosis |
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Components |
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-Supramolecule #1: Cryo-EM structure of WT KatG from M. tuberculosis
Supramolecule | Name: Cryo-EM structure of WT KatG from M. tuberculosis / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Molecular weight | Theoretical: 161210 kDa/nm |
-Macromolecule #1: Catalase-peroxidase
Macromolecule | Name: Catalase-peroxidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: catalase-peroxidase |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Molecular weight | Theoretical: 80.687609 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPEQHPPITE TTTGAASNGC PVVGHMKYPV EGGGNQDWWP NRLNLKVLHQ NPAVADPMGA AFDYAAEVAT IDVDALTRDI EEVMTTSQP WWPADYGHYG PLFIRMAWHA AGTYRIHDGR GGAGGGMQRF APLNSWPDNA SLDKARRLLW PVKKKYGKKL S WADLIVFA ...String: MPEQHPPITE TTTGAASNGC PVVGHMKYPV EGGGNQDWWP NRLNLKVLHQ NPAVADPMGA AFDYAAEVAT IDVDALTRDI EEVMTTSQP WWPADYGHYG PLFIRMAWHA AGTYRIHDGR GGAGGGMQRF APLNSWPDNA SLDKARRLLW PVKKKYGKKL S WADLIVFA GNCALESMGF KTFGFGFGRV DQWEPDEVYW GKEATWLGDE RYSGKRDLEN PLAAVQMGLI YVNPEGPNGN PD PMAAAVD IRETFRRMAM NDVETAALIV GGHTFGKTHG AGPADLVGPE PEAAPLEQMG LGWKSSYGTG TGKDAITSGI EVV WTNTPT KWDNSFLEIL YGYEWELTKS PAGAWQYTAK DGAGAGTIPD PFGGPGRSPT MLATDLSLRV DPIYERITRR WLEH PEELA DEFAKAWYKL IHRDMGPVAR YLGPLVPKQT LLWQDPVPAV SHDLVGEAEI ASLKSQIRAS GLTVSQLVST AWAAA SSFR GSDKRGGANG GRIRLQPQVG WEVNDPDGDL RKVIRTLEEI QESFNSAAPG NIKVSFADLV VLGGCAAIEK AAKAAG HNI TVPFTPGRTD ASQEQTDVES FAVLEPKADG FRNYLGKGNP LPAEYMLLDK ANLLTLSAPE MTVLVGGLRV LGANYKR LP LGVFTEASES LTNDFFVNLL DMGITWEPSP ADDGTYQGKD GSGKVKWTGS RVDLVFGSNS ELRALVEVYG ADDAQPKF V QDFVAAWDKV MNLDRFDVR UniProtKB: Catalase-peroxidase |
-Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ChemComp-HEM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Material: COPPER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.29 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |