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- EMDB-33363: Cryo-EM map of cystathionine beta-synthase of Mycobacterium tuber... -
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Open data
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Basic information
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Title | Cryo-EM map of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine and serine. | |||||||||||||||||||||||||||||||||||||||
![]() | Cryo-EM map of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine and serine. | |||||||||||||||||||||||||||||||||||||||
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![]() | Cystathionine beta-synthase / transsulfuration / LYASE | |||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() cystathionine beta-synthase / cysteine biosynthetic process via cystathionine / cystathionine beta-synthase activity / cysteine synthase activity / cysteine biosynthetic process from serine / peptidoglycan-based cell wall / pyridoxal phosphate binding / extracellular region / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.25 Å | |||||||||||||||||||||||||||||||||||||||
![]() | Bandyopadhyay P / Pramanick I / Biswas R / Sabarinath PS / Sreedharan S / Singh S / Rajmani R / Laxman S / Dutta S / Singh A | |||||||||||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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
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Downloads & links
-EMDB archive
Map data | ![]() | 49.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.7 KB 17.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 104.6 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 49.4 MB 49.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xoyMC ![]() 7xnzC ![]() 7xohC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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 |
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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 / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-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: ![]() |
Molecular weight | Theoretical: 50.284848 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 UniProtKB: Probable cystathionine beta-synthase Rv1077 |
-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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |