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- PDB-7xnz: Native cystathionine beta-synthase of Mycobacterium tuberculosis. -

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Basic information

Entry
Database: PDB / ID: 7xnz
TitleNative cystathionine beta-synthase of Mycobacterium tuberculosis.
ComponentsPutative cystathionine beta-synthase Rv1077
KeywordsLYASE / cystathionine beta-synthase / transsulfuration
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
PYRIDOXAL-5'-PHOSPHATE / Probable cystathionine beta-synthase Rv1077
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBandyopadhyay, P. / Pramanick, I. / Biswas, R. / Sabarinath, P.S. / Sreedharan, S. / Singh, S. / Rajmani, R. / Laxman, S. / Dutta, S. / Singh, A.
Funding support India, 13items
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
DepositionApr 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Putative cystathionine beta-synthase Rv1077
A: Putative cystathionine beta-synthase Rv1077
C: Putative cystathionine beta-synthase Rv1077
D: Putative cystathionine beta-synthase Rv1077
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,1288
Polymers201,1394
Non-polymers9894
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Putative cystathionine beta-synthase Rv1077 / Beta-thionase / Serine sulfhydrase


Mass: 50284.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cbs, Rv1077 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WP51, cystathionine beta-synthase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cystathionine beta-synthase enzyme of Mycobacterium tuberculosis.
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3900 nm / Nominal defocus min: 2200 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178599 / Symmetry type: POINT

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