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- EMDB-63589: Imidazole glycerol phosphate dehydratase from Mycobacterium tuber... -

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Basic information

Entry
Database: EMDB / ID: EMD-63589
TitleImidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, in complex with aminotriazole
Map dataCombined, sharpened map
Sample
  • Complex: Mycobacterium tuberculosis HisB with 3TR
    • Protein or peptide: Imidazoleglycerol-phosphate dehydratase
  • Ligand: MANGANESE (II) ION
  • Ligand: 3-AMINO-1,2,4-TRIAZOLE
Keywordshistidine pathway / dehydratase / Mycobacterium tuberculosis / LYASE
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Imidazoleglycerol-phosphate dehydratase signature 1. / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase, conserved site / Imidazole glycerol phosphate dehydratase domain superfamily / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase signature 2. / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRaina R / Kar D / Singla M / Tiwari S / Kumari S / Aneja S / Kumar V / Banerjee S / Goyal S / Pal RK ...Raina R / Kar D / Singla M / Tiwari S / Kumari S / Aneja S / Kumar V / Banerjee S / Goyal S / Pal RK / Vinothkumar KR / Biswal BK
Funding support India, 4 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/HRD/TIF/09/02/2021-22 India
Department of Biotechnology (DBT, India)BT/PR29075/BRB/10/1699/2018 India
Department of Biotechnology (DBT, India)BT/PR40325/BTIS/137/1/2020 India
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2025
Title: Cryo-EM structures of Mycobacterium tuberculosis imidazole glycerol phosphate dehydratase in the apo state and in the presence of small molecules.
Authors: Rahul Raina / Deepsikha Kar / Mohini Singla / Satish Tiwari / Swati Kumari / Sonanjali Aneja / Varun Kumar / Soumya Banerjee / Shivika Goyal / Ravi Kant Pal / Kutti R Vinothkumar / Bichitra Biswal /
Abstract: Unlike humans, Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, has a de novo histidine-biosynthesis pathway. The enzyme imidazole glycerol phosphate dehydratase (IGPD), ...Unlike humans, Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, has a de novo histidine-biosynthesis pathway. The enzyme imidazole glycerol phosphate dehydratase (IGPD), which catalyses the conversion of imidazole glycerol phosphate to imidazole acetol phosphate, has been studied extensively from various organisms and has become a major target for the development of antibacterial, antiweed and antifungal small molecules. In our previous studies, we have shown that in crystals IGPD forms a 24-mer oligomeric state in which the monomers are arranged in 432 symmetry. In order to gain insights into the oligomeric state of Mtb IGPD in solution, we determined cryogenic sample electron microscopy (cryo-EM) structures of apo IGPD at 2.2 and 3.1 Å resolution. In addition, we also determined the cryo-EM structure of IGPD in the presence of 3-amino-1,2,4-triazole (ATZ) to 2.8 Å resolution. The results of this work, which corroborate those from the crystallographic studies, indicate that IGPD forms a homo-oligomeric structure in solution comprising of 24 subunits. ATZ binds in the active-site pocket of the enzyme, which is located at the interface of three monomers and tethers 24 ATZ molecules. The results of this study suggest that cryo-EM, in addition to being a rapidly evolving and complementary imaging technology for elucidating 3D structures of biological macromolecules, can be useful in pinpointing the mode of binding small molecules of low mass (here ∼85 Da) and mapping protein-ligand interactions, which could assist in the design of accurate (high-potency) inhibitors.
History
DepositionFeb 28, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63589.png

Downloads & links

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Map

FileDownload / File: emd_63589.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined, sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 250 pix.
= 267.5 Å		1.07 Å/pix.
x 250 pix.
= 267.5 Å		1.07 Å/pix.
x 250 pix.
= 267.5 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: 0.075
Minimum - Maximum-0.1934279 - 0.39081174
Average (Standard dev.)0.00012228216 (±0.02045679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 267.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: One of the half maps

Fileemd_63589_half_map_1.map
AnnotationOne of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the half maps

Fileemd_63589_half_map_2.map
AnnotationOne of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium tuberculosis HisB with 3TR

EntireName: Mycobacterium tuberculosis HisB with 3TR
Components
  • Complex: Mycobacterium tuberculosis HisB with 3TR
    • Protein or peptide: Imidazoleglycerol-phosphate dehydratase
  • Ligand: MANGANESE (II) ION
  • Ligand: 3-AMINO-1,2,4-TRIAZOLE

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Supramolecule #1: Mycobacterium tuberculosis HisB with 3TR

SupramoleculeName: Mycobacterium tuberculosis HisB with 3TR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: An oligomer of 24 subunits
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 550 KDa

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Macromolecule #1: Imidazoleglycerol-phosphate dehydratase

MacromoleculeName: Imidazoleglycerol-phosphate dehydratase / type: protein_or_peptide / ID: 1
Details: The enzyme was expressed with a Histag at the N-terminus but not observed in the experiment. The C-terminal residues are also not observed in the experiment. Uniparc ID is UPI000012C861.
Number of copies: 24 / Enantiomer: LEVO / EC number: imidazoleglycerol-phosphate dehydratase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 23.633516 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MHHHHHHTTT QTAKASRRAR IERRTRESDI VIELDLDGTG QVAVDTGVPF YDHMLTALGS HASFDLTVRA TGDVEIEAHH TIEDTAIAL GTALGQALGD KRGIRRFGDA FIPMDETLAH AAVDLSGRPY CVHTGEPDHL QHTTIAGSSV PYHTVINRHV F ESLAANAR ...String:
MHHHHHHTTT QTAKASRRAR IERRTRESDI VIELDLDGTG QVAVDTGVPF YDHMLTALGS HASFDLTVRA TGDVEIEAHH TIEDTAIAL GTALGQALGD KRGIRRFGDA FIPMDETLAH AAVDLSGRPY CVHTGEPDHL QHTTIAGSSV PYHTVINRHV F ESLAANAR IALHVRVLYG RDPHHITEAQ YKAVARALRQ AVEPDPRVSG VPSTKGAL

UniProtKB: Imidazoleglycerol-phosphate dehydratase

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Macromolecule #2: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 48 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #3: 3-AMINO-1,2,4-TRIAZOLE

MacromoleculeName: 3-AMINO-1,2,4-TRIAZOLE / type: ligand / ID: 3 / Number of copies: 24 / Formula: 3TR
Molecular weightTheoretical: 84.08 Da
Chemical component information

ChemComp-3TR:
3-AMINO-1,2,4-TRIAZOLE / inhibitor*YM

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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

Concentration1.2 mg/mL
BufferpH: 8.5
Component:
ConcentrationNameFormula
20.0 mMTris
200.0 mMSodium ChlorideNaCl
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
DetailsEnzyme was incubated with 10 fold excess of 3TR and this mixture was directly used for freezing

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 60.0 sec. / Average electron dose: 27.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 130841 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 35.0 µm / Nominal defocus min: 12.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 189390
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1), RELION) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-intio using Relion
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 23789
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4lpf


Chain - Chain ID: A / Chain - Residue range: 10-199 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 133.9
Output model

PDB-9m2q:
Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, in complex with aminotriazole

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