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 7XOH | pdb_00007xoh

Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7XOH

This is version 2.0 of the entry. See complete history. 

Literature

S-Adenosylmethionine-responsive cystathionine beta-synthase modulates sulfur metabolism and redox balance in Mycobacterium tuberculosis.

Bandyopadhyay, P., Pramanick, I., Biswas, R., Ps, S., Sreedharan, S., Singh, S., Rajmani, R.S., Laxman, S., Dutta, S., Singh, A.

(2022) Sci Adv 8: eabo0097-eabo0097

  • DOI: https://doi.org/10.1126/sciadv.abo0097
  • Primary Citation Related Structures: 
    7XNZ, 7XOH, 7XOY

  • PubMed Abstract: 

    Methionine and cysteine metabolisms are important for the survival and pathogenesis of Mycobacterium tuberculosis ( Mtb ). 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 ( Mtb Cbs) in Mtb . We demonstrated that Mtb Cbs is a heme-less, pyridoxal-5'-phosphate-containing enzyme, allosterically activated by S -adenosylmethionine (SAM). The atomic model of Mtb Cbs in its native and SAM-bound conformations revealed a unique mode of SAM-dependent allosteric activation. Further, SAM stabilized Mtb Cbs by sterically occluding proteasomal degradation, which was crucial for supporting methionine and redox metabolism in Mtb . Genetic deficiency of Mtb Cbs reduced Mtb survival upon homocysteine overload in vitro, inside macrophages, and in mice coinfected with HIV. Thus, the Mtb Cbs-SAM axis constitutes an important mechanism of coordinating sulfur metabolism in Mtb .


  • Organizational Affiliation: 
    • Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India.

Macromolecule Content 

  • Total Structure Weight: 202.05 kDa 
  • Atom Count: 13,524 
  • Modeled Residue Count: 1,832 
  • Deposited Residue Count: 1,912 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable cystathionine beta-synthase Rv1077A [auth B],
B [auth A],
C,
D
478Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: cbs, Rv1077
EC: 4.2.1.22
UniProt
Find proteins for P9WP51 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WP51 
Go to UniProtKB:  P9WP51
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WP51
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A [auth B],
B [auth A],
C,
D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaIA/S/16/2/502700
Department of Biotechnology (DBT, India)IndiaBT/PR13522/COE/34/27/2015
Department of Biotechnology (DBT, India)IndiaBT/PR29098/Med/29/1324/2018
Department of Biotechnology (DBT, India)IndiaBT/HRD/NBA/39/07/2018-19
Department of Biotechnology (DBT, India)IndiaBT/PR39308/DRUG/134/86/2021
Department of Biotechnology (DBT, India)India22-0905-0006-05-987-436
Science and Engineering Research Board (SERB)IndiaSB/S2/RJN-145/2015
Science and Engineering Research Board (SERB)IndiaSERB-EMR/2016/000608
Department of Biotechnology (DBT, India)IndiaBT/PR25580/BRB/10/1619/2017
Department of Biotechnology (DBT, India)IndiaIA/E/19/1/504978
Department of Biotechnology (DBT, India)IndiaBT/INF/22/SP22844/2017
Department of Science & Technology (DST, India)IndiaSR/FST/LSII-039/2015
Department of Biotechnology (DBT, India)IndiaDBT/PR12422/MED/31/287/2014

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 2.0: 2025-06-25
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary