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- PDB-26fv: Tetrameric cystathionine beta-synthase of Mycobacterium tuberculo... -

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Basic information

Entry
Database: PDB / ID: 26fv
TitleTetrameric cystathionine beta-synthase of Mycobacterium tuberculosis bound to AOAA
ComponentsProbable cystathionine beta-synthase Rv1077
KeywordsLYASE / Inhibitor / Complex
Function / homology
Function and homology information


cystathionine beta-synthase / cystathionine beta-synthase activity / : / cysteine synthase activity / : / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE / Probable cystathionine beta-synthase Rv1077
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsRoy, A. / Polepalli, S. / Mondal, B. / Dutta, S.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)(BT/INF/22/SP22844/2017) India
Department of Science & Technology (DST, India)(SR/FST/LSII-039/2015) India
CitationJournal: Int J Biol Macromol / Year: 2026
Title: Molecular insights into inhibitor action on the catalytic activity of Mycobacterium tuberculosis cystathionine β-synthase enzyme.
Authors: Sainath Polepalli / Anupam Roy / Bapan Mondal / Amit Singh / Somnath Dutta /
Abstract: Tuberculosis (TB) remains a major global health threat, with Mycobacterium tuberculosis (Mtb) infecting nearly a quarter of the global population. Drug-resistant TB and HIV-TB co-infections emphasize ...Tuberculosis (TB) remains a major global health threat, with Mycobacterium tuberculosis (Mtb) infecting nearly a quarter of the global population. Drug-resistant TB and HIV-TB co-infections emphasize the need for novel therapeutic approaches targeting essential metabolic pathways. Here, we investigated Mtb cystathionine β-synthase (MtbCBS), a pyridoxal 5'-phosphate (PLP) dependent enzyme critical for sulfur metabolism and redox regulation, owing to its potential as a therapeutic target. Despite growing efforts to develop novel therapeutics, the widely used inhibitor aminooxy acetic acid (AOAA) is a non-specific inhibitor of all PLP-dependent enzymes, and the precise structural and mechanistic basis for its activity and specificity remains poorly understood. We present the high-resolution cryo-EM structure of full-length tetrameric MtbCBS in complex with AOAA, revealing a stable PLP-inhibitor adduct stabilized by two highly conserved active-site residues, T75 and Q147. This integrated approach employs cryo-EM, molecular dynamics (MD) simulations, Density Functional Theory (DFT) calculations, and comparative inhibition studies to reveal the molecular basis and determinants governing PLP-enzyme MtbCBS inhibition by AOAA. Through molecular mimic studies, we identified precise structural and electronic features of the inhibitor candidate that are critical for inhibition efficiency. These findings provide a mechanistic rationale for MtbCBS inhibition, and the unexplored roles of these key residues can be considered in the design of next-generation inhibitors targeting CBS enzymes implicated in infectious diseases, cancer, and neurological disorders.
History
DepositionApr 29, 2026Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 9, 2026ID: 9U7O
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)202,4288
Polymers201,1394
Non-polymers1,2894
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Probable 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 BL21(DE3) (bacteria) / References: UniProt: P9WP51, cystathionine beta-synthase
#2: Chemical
ChemComp-IK2 / 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: The ternary complex of AOAA-bound to MtbCBS / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89896 / Symmetry type: POINT
RefinementHighest resolution: 3.34 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00213820
ELECTRON MICROSCOPYf_angle_d0.48618796
ELECTRON MICROSCOPYf_dihedral_angle_d11.0055024
ELECTRON MICROSCOPYf_chiral_restr0.0412104
ELECTRON MICROSCOPYf_plane_restr0.0032476

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