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- EMDB-33348: Cryo-EM map of cystathionine beta-synthase of Mycobacterium tuber... -

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Basic information

Entry
Database: EMDB / ID: EMD-33348
TitleCryo-EM map of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.
Map dataCryo-EM map of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.
Sample
  • Complex: Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.
    • Protein or peptide: Putative cystathionine beta-synthase Rv1077
  • Ligand: PYRIDOXAL-5'-PHOSPHATE
Function / homology
Function and homology information


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
Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / : / Domain in cystathionine beta-synthase and other proteins. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Probable cystathionine beta-synthase Rv1077
Similarity search - Component
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBandyopadhyay P / Pramanick I / Biswas R / Sabarinath PS / Sreedharan S / Singh S / Rajmani R / Laxman S / Dutta S / Singh A
Funding support India, 13 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)IA/S/16/2/502700 India
Department of Biotechnology (DBT, India)BT/PR13522/COE/34/27/2015 India
Department of Biotechnology (DBT, India)BT/PR29098/Med/29/1324/2018 India
Department of Biotechnology (DBT, India)BT/HRD/NBA/39/07/2018-19 India
Department of Biotechnology (DBT, India)BT/PR39308/DRUG/134/86/2021 India
Department of Biotechnology (DBT, India)22-0905-0006-05-987-436 India
Science and Engineering Research Board (SERB)SB/S2/RJN-145/2015 India
Science and Engineering Research Board (SERB)SERB-EMR/2016/000608 India
Department of Biotechnology (DBT, India)BT/PR25580/BRB/10/1619/2017 India
Department of Biotechnology (DBT, India)IA/E/19/1/504978 India
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: 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
DepositionMay 1, 2022-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33348.png

Downloads & links

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Map

FileDownload / File: emd_33348.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0348
Minimum - Maximum-0.2185174 - 0.30923396
Average (Standard dev.)-1.7835843e-06 (±0.010710174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 of cystathionine beta-synthase of Mycobacterium...

Fileemd_33348_half_map_1.map
AnnotationHalf map 1 of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of cystathionine beta-synthase of Mycobacterium...

Fileemd_33348_half_map_2.map
AnnotationHalf map 2 of cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cystathionine beta-synthase of Mycobacterium tuberculosis in the ...

EntireName: Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.
Components
  • Complex: Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.
    • Protein or peptide: Putative cystathionine beta-synthase Rv1077
  • Ligand: PYRIDOXAL-5'-PHOSPHATE

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Supramolecule #1: Cystathionine beta-synthase of Mycobacterium tuberculosis in the ...

SupramoleculeName: Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)

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Macromolecule #1: Putative cystathionine beta-synthase Rv1077

MacromoleculeName: Putative cystathionine beta-synthase Rv1077 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: cystathionine beta-synthase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 50.284848 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: PYRIDOXAL-5'-PHOSPHATE

MacromoleculeName: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: PLP
Molecular weightTheoretical: 247.142 Da
Chemical component information

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.9 µm / Nominal defocus min: 2.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146444
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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