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- PDB-7xoh: Cystathionine beta-synthase of Mycobacterium tuberculosis in the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xoh | ||||||||||||||||||||||||||||||||||||||||||
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Title | Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine. | ||||||||||||||||||||||||||||||||||||||||||
![]() | Putative cystathionine beta-synthase Rv1077 | ||||||||||||||||||||||||||||||||||||||||||
![]() | LYASE / cystathionine beta-synthase / transsulfuration / S-adenosylmethionine | ||||||||||||||||||||||||||||||||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||||||||||||||||||||||||||
![]() | Bandyopadhyay, P. / Pramanick, I. / Biswas, R. / Sabarinath, P.S. / 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 295.3 KB | Display | ![]() |
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PDB format | ![]() | 245.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 33348MC ![]() 7xnzC ![]() 7xoyC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 50284.848 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cbs, Rv1077 / Production host: ![]() ![]() #2: Chemical | ChemComp-PLP / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cystathionine beta-synthase of Mycobacterium tuberculosis in the presence of S-adenosylmethionine. Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3900 nm / Nominal defocus min: 2200 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146444 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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