+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11689 | |||||||||
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Title | T275P after heme uptake from M. tuberculosis | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Heme / Catalase / Peroxidase enzyme / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / catalase activity / positive regulation of DNA repair / NADPH binding / peptidoglycan-based cell wall / hydrogen peroxide catabolic process / peroxidase activity ...oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / catalase activity / positive regulation of DNA repair / NADPH binding / peptidoglycan-based cell wall / hydrogen peroxide catabolic process / peroxidase activity / cellular response to hydrogen peroxide / response to oxidative stress / response to antibiotic / heme binding / extracellular region / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.56 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_11689.map.gz | 87.8 MB | EMDB map data format | |
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Header (meta data) | emd-11689-v30.xml emd-11689.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11689_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_11689.png | 5.2 KB | ||
Filedesc metadata | emd-11689.cif.gz | 5.4 KB | ||
Others | emd_11689_half_map_1.map.gz emd_11689_half_map_2.map.gz | 86.1 MB 86.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11689 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11689 | HTTPS FTP |
-Validation report
Summary document | emd_11689_validation.pdf.gz | 992.9 KB | Display | EMDB validaton report |
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Full document | emd_11689_full_validation.pdf.gz | 992.5 KB | Display | |
Data in XML | emd_11689_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | emd_11689_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11689 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11689 | HTTPS FTP |
-Related structure data
Related structure data | 7aa3MC 6zjiC 7a2iC 7a7aC 7a7cC 7a8zC 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_11689.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_11689_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11689_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homodimer of KatG from M.tuberculosis
Entire | Name: Homodimer of KatG from M.tuberculosis |
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Components |
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-Supramolecule #1: Homodimer of KatG from M.tuberculosis
Supramolecule | Name: Homodimer of KatG from M.tuberculosis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
-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: 80.683617 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 GGHTFGKPHG 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 |
-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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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |