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Yorodumi- EMDB-33363: Cryo-EM map of cystathionine beta-synthase of Mycobacterium tuber... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33363 | |||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM map of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine and serine. | |||||||||||||||||||||||||||||||||||||||
Map data | Cryo-EM map of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine and serine. | |||||||||||||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / cysteine synthase activity / cysteine biosynthetic process from serine / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.25 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Bandyopadhyay P / Pramanick I / Biswas R / Sabarinath PS / Sreedharan S / Singh S / Rajmani R / Laxman S / Dutta S / Singh A | |||||||||||||||||||||||||||||||||||||||
Funding support | India, 12 items
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Citation | Journal: Sci Adv / Year: 2022 Title: -Adenosylmethionine-responsive cystathionine β-synthase modulates sulfur metabolism and redox balance in . Authors: Parijat Bandyopadhyay / Ishika Pramanick / Rupam Biswas / Sabarinath Ps / Sreesa Sreedharan / Shalini Singh / Raju S Rajmani / Sunil Laxman / Somnath Dutta / Amit Singh / Abstract: Methionine and cysteine metabolisms are important for the survival and pathogenesis of (). The transsulfuration pathway converts methionine to cysteine and represents an important link between ...Methionine and cysteine metabolisms are important for the survival and pathogenesis of (). The transsulfuration pathway converts methionine to cysteine and represents an important link between antioxidant and methylation metabolism in diverse organisms. Using a combination of biochemistry and cryo-electron microscopy, we characterized the first enzyme of the transsulfuration pathway, cystathionine β-synthase (Cbs) in . We demonstrated that Cbs is a heme-less, pyridoxal-5'-phosphate-containing enzyme, allosterically activated by -adenosylmethionine (SAM). The atomic model of Cbs in its native and SAM-bound conformations revealed a unique mode of SAM-dependent allosteric activation. Further, SAM stabilized Cbs by sterically occluding proteasomal degradation, which was crucial for supporting methionine and redox metabolism in . Genetic deficiency of Cbs reduced survival upon homocysteine overload in vitro, inside macrophages, and in mice coinfected with HIV. Thus, the Cbs-SAM axis constitutes an important mechanism of coordinating sulfur metabolism in . | |||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33363.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-33363-v30.xml emd-33363.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33363_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_33363.png | 104.6 KB | ||
Others | emd_33363_half_map_1.map.gz emd_33363_half_map_2.map.gz | 49.4 MB 49.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33363 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33363 | HTTPS FTP |
-Related structure data
Related structure data | 7xoyMC 7xnzC 7xohC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33363.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM map of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine and serine. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.17 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map 2 of cystathionine beta-synthase of Mycobacterium...
File | emd_33363_half_map_1.map | ||||||||||||
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Annotation | Half map 2 of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine and serine. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of cystathionine beta-synthase of Mycobacterium...
File | emd_33363_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine and serine. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cystathionine beta-synthase of Mycobacterium tuberculosis in the ...
Entire | Name: Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine and serine. |
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Components |
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-Supramolecule #1: Cystathionine beta-synthase of Mycobacterium tuberculosis in the ...
Supramolecule | Name: Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine and serine. type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) |
-Macromolecule #1: Putative cystathionine beta-synthase Rv1077
Macromolecule | Name: Putative cystathionine beta-synthase Rv1077 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: cystathionine beta-synthase |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 50.284848 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARIAQHISE LIGGTPLVRL NSVVPDGAGT VAAKVEYLNP GGSSKDRIAV KMIEAAEASG QLKPGGTIVE PTSGNTGVGL ALVAQRRGY KCVFVCPDKV SEDKRNVLIA YGAEVVVCPT AVPPHDPASY YSVSDRLVRD IDGAWKPDQY ANPEGPASHY V TTGPEIWA ...String: MARIAQHISE LIGGTPLVRL NSVVPDGAGT VAAKVEYLNP GGSSKDRIAV KMIEAAEASG QLKPGGTIVE PTSGNTGVGL ALVAQRRGY KCVFVCPDKV SEDKRNVLIA YGAEVVVCPT AVPPHDPASY YSVSDRLVRD IDGAWKPDQY ANPEGPASHY V TTGPEIWA DTEGKVTHFV AGIGTGGTIT GAGRYLKEVS GGRVRIVGAD PEGSVYSGGA GRPYLVEGVG EDFWPAAYDP SV PDEIIAV SDSDSFDMTR RLAREEAMLV GGSCGMAVVA ALKVAEEAGP DALIVVLLPD GGRGYMSKIF NDAWMSSYGF LRS RLDGST EQSTVGDVLR RKSGALPALV HTHPSETVRD AIGILREYGV SQMPVVGAEP PVMAGEVAGS VSERELLSAV FEGR AKLAD AVSAHMSPPL RMIGAGELVS AAGKALRDWD ALMVVEEGKP VGVITRYDLL GFLSEGAGRR KLAAALEHHH HHH |
-Macromolecule #2: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
Macromolecule | Name: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE type: ligand / ID: 2 / Number of copies: 4 / Formula: PLS |
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Molecular weight | Theoretical: 336.235 Da |
Chemical component information | ChemComp-PLS: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |