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- EMDB-48789: Cryo EM structure of the Open tetramer of Rv2531c from Mycobacter... -

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Basic information

Entry
Database: EMDB / ID: EMD-48789
TitleCryo EM structure of the Open tetramer of Rv2531c from Mycobacterium Tuberculosis.
Map dataThis a homotetramer of Rv2531c.
Sample
  • Complex: Rv2531c open tetramer
    • Protein or peptide: Probable amino acid decarboxylase
Keywordsglutamate decarboxylase / LYASE
Function / homology: / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / transaminase activity / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Probable amino acid decarboxylase
Function and homology information
Biological speciesMycobacteriunm Tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGupta J / Izard T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Biol Chem / Year: 2025
Title: CryoEM structure of Rv2531c reveals cofactor-induced tetramer-dimer transition in a tuberculin amino acid decarboxylase.
Authors: Jyoti Gupta / Tina Izard /
Abstract: The survival of Mycobacteriumtuberculosis relies on its ability to adapt to dynamic and hostile host environments. Amino acid decarboxylases play a crucial role in these adaptations, but their ...The survival of Mycobacteriumtuberculosis relies on its ability to adapt to dynamic and hostile host environments. Amino acid decarboxylases play a crucial role in these adaptations, but their structural and mechanistic properties are not fully understood. Bioinformatic analyses revealed that these enzymes exist in three distinct forms based on their domain organization. We used cryoEM at 2.76 Å resolution to show that Rv2531c exhibits unexpected oligomeric and conformational flexibility. The enzyme forms a tetramer with distinct open and closed conformations in its apo state, suggesting dynamic intersubunit interactions. Upon binding pyridoxal 5'-phosphate, the enzyme undergoes a dramatic structural rearrangement, transitioning into a dimer. These findings reveal a novel mechanism of oligomeric plasticity. We also uncover an amino-terminal domain that might play a role in this process. Our results provide critical insights into the structural adaptations that support bacterial persistence under intracellular stress. By elucidating the apo and pyridoxal 5'-phosphate-bound states of Rv2531c, we contribute to a deeper understanding of how M. tuberculosis navigates its challenging intracellular environment. These insights into the unique structural features of Rv2531c offer a foundation for targeting metabolic resilience in tuberculosis and open avenues for future studies on the role of this domain in pathogenesis.
History
DepositionJan 24, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48789.png

Downloads & links

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Map

FileDownload / File: emd_48789.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis a homotetramer of Rv2531c.
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 368.64 Å		0.72 Å/pix.
x 512 pix.
= 368.64 Å		0.72 Å/pix.
x 512 pix.
= 368.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.40946013 - 0.5939572
Average (Standard dev.)0.0001335011 (±0.0141860265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 368.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48789_msk_1.map
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Additional map: #1

Fileemd_48789_additional_1.map
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Half map: This is the half Map A

Fileemd_48789_half_map_1.map
AnnotationThis is the half Map A
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Half map: This is the half Map B

Fileemd_48789_half_map_2.map
AnnotationThis is the half Map B
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Sample components

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Entire : Rv2531c open tetramer

EntireName: Rv2531c open tetramer
Components
  • Complex: Rv2531c open tetramer
    • Protein or peptide: Probable amino acid decarboxylase

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Supramolecule #1: Rv2531c open tetramer

SupramoleculeName: Rv2531c open tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacteriunm Tuberculosis (bacteria)
Molecular weightTheoretical: 440 KDa

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Macromolecule #1: Probable amino acid decarboxylase

MacromoleculeName: Probable amino acid decarboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 106.150781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNPNSVRPRR LHVSALAAVA NPSYTRLDTW NLLDDACRHL AEVDLAGLDT THDVARAKRL MDRIGAYERY WLYPGAQNLA TFRAHLDSH STVRLTEEVS LAVRLLSEYG DRTALFDTSA SLAEQELVAQ AKQQQFYTVL LADDSPATAP DSLAECLRQL R NPADEVQF ...String:
MNPNSVRPRR LHVSALAAVA NPSYTRLDTW NLLDDACRHL AEVDLAGLDT THDVARAKRL MDRIGAYERY WLYPGAQNLA TFRAHLDSH STVRLTEEVS LAVRLLSEYG DRTALFDTSA SLAEQELVAQ AKQQQFYTVL LADDSPATAP DSLAECLRQL R NPADEVQF ELLVVASIED AITAVALNGE IQAAIIRHDL PLRSRDRVPL MTTLLGTDGD EAVANETHDW VECAEWIREL RP HIDLYLL TDESIAAETQ DEPDVYDRTF YRLNDVTDLH STVLAGLRNR YATPFFDALR AYAAAPVGQF HALPVARGAS IFN SKSLHD MGEFYGRNIF MAETSTTSGG LDSLLDPHGN IKTAMDKAAV TWNANQTYFV TNGTSTANKI VVQALTRPGD IVLI DRNCH KSHHYGLVLA GAYPMYLDAY PLPQYAIYGA VPLRTIKQAL LDLEAAGQLH RVRMLLLTNC TFDGVVYNPR RVMEE VLAI KPDICFLWDE AWYAFATAVP WARQRTAMIA AERLEQMLST AEYAEEYRNW CASMDGVDRS EWVDHRLLPD PNRARV RVY ATHSTHKSLS ALRQASMIHV RDQDFKALTR DAFGEAFLTH TSTSPNQQLL ASLDLARRQV DIEGFELVRH VYNMALV FR HRVRKDRLIS KWFRILDESD LVPDAFRSST VSSYRQVRQG ALADWNEAWR SDQFVLDPTR LTLFIGATGM NGYDFREK I LMERFGIQIN KTSINSVLLI FTIGVTWSSV HYLLDVLRRV AIDLDRSQKA ASGADLALHR RHVEEITQDL PHLPDFSEF DLAFRPDDAS SFGDMRSAFY AGYEEADREY VQIGLAGRRL AEGKTLVSTT FVVPYPPGFP VLVPGQLVSK EIIYFLAQLD VKEIHGYNP DLGLSVFTQA ALARMEAARN AVATVGAALP AFEVPRDASA LNGTVNGDSV LQGVAEDA

UniProtKB: Probable amino acid decarboxylase

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 113770
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9n0p:
Cryo EM structure of the Open tetramer of Rv2531c from Mycobacterium Tuberculosis.

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