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- EMDB-48788: CryoEM structure of Rv2531c dimer from Mycobacterium tuberculosis -

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Basic information

Entry
Database: EMDB / ID: EMD-48788
TitleCryoEM structure of Rv2531c dimer from Mycobacterium tuberculosis
Map dataThis is a homodimer with C2 symmetry
Sample
  • Complex: Rv2531c in complex with pyridoxal 5'-phosphate
    • Protein or peptide: Probable amino acid decarboxylase
  • Ligand: PYRIDOXAL-5'-PHOSPHATE
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 speciesMycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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_48788.png

Downloads & links

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Map

FileDownload / File: emd_48788.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a homodimer with C2 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.135
Minimum - Maximum-1.42247 - 2.0088096
Average (Standard dev.)0.000013507236 (±0.033226073)
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_48788_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: This is a homodimer with C2 symmetry

Fileemd_48788_additional_1.map
AnnotationThis is a homodimer with C2 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is the Half Map A.

Fileemd_48788_half_map_1.map
AnnotationThis is the Half Map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is the Half Map B.

Fileemd_48788_half_map_2.map
AnnotationThis is the Half Map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rv2531c in complex with pyridoxal 5'-phosphate

EntireName: Rv2531c in complex with pyridoxal 5'-phosphate
Components
  • Complex: Rv2531c in complex with pyridoxal 5'-phosphate
    • Protein or peptide: Probable amino acid decarboxylase
  • Ligand: PYRIDOXAL-5'-PHOSPHATE

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Supramolecule #1: Rv2531c in complex with pyridoxal 5'-phosphate

SupramoleculeName: Rv2531c in complex with pyridoxal 5'-phosphate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 210 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 104.501852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ALAAVANPSY TRLDTWNLLD DACRHLAEVD LAGLDTTHDV ARAKRLMDRI GAYERYWLYP GAQNLATFRA HLDSHSTVRL TEEVSLAVR LLSEYGDRTA LFDTSASLAE QELVAQAKQQ QFYTVLLADD SPATAPDSLA ECLRQLRNPA DEVQFELLVV A SIEDAITA ...String:
ALAAVANPSY TRLDTWNLLD DACRHLAEVD LAGLDTTHDV ARAKRLMDRI GAYERYWLYP GAQNLATFRA HLDSHSTVRL TEEVSLAVR LLSEYGDRTA LFDTSASLAE QELVAQAKQQ QFYTVLLADD SPATAPDSLA ECLRQLRNPA DEVQFELLVV A SIEDAITA VALNGEIQAA IIRHDLPLRS RDRVPLMTTL LGTDGDEAVA NETHDWVECA EWIRELRPHI DLYLLTDESI AA ETQDEPD VYDRTFYRLN DVTDLHSTVL AGLRNRYATP FFDALRAYAA APVGQFHALP VARGASIFNS KSLHDMGEFY GRN IFMAET STTSGGLDSL LDPHGNIKTA MDKAAVTWNA NQTYFVTNGT STANKIVVQA LTRPGDIVLI DRNCHKSHHY GLVL AGAYP MYLDAYPLPQ YAIYGAVPLR TIKQALLDLE AAGQLHRVRM LLLTNCTFDG VVYNPRRVME EVLAIKPDIC FLWDE AWYA FATAVPWARQ RTAMIAAERL EQMLSTAEYA EEYRNWCASM DGVDRSEWVD HRLLPDPNRA RVRVYATHST HKSLSA LRQ ASMIHVRDQD FKALTRDAFG EAFLTHTSTS PNQQLLASLD LARRQVDIEG FELVRHVYNM ALVFRHRVRK DRLISKW FR ILDESDLVPD AFRSSTVSSY RQVRQGALAD WNEAWRSDQF VLDPTRLTLF IGATGMNGYD FREKILMERF GIQINKTS I NSVLLIFTIG VTWSSVHYLL DVLRRVAIDL DRSQKAASGA DLALHRRHVE EITQDLPHLP DFSEFDLAFR PDDASSFGD MRSAFYAGYE EADREYVQIG LAGRRLAEGK TLVSTTFVVP YPPGFPVLVP GQLVSKEIIY FLAQLDVKEI HGYNPDLGLS VFTQAALAR MEAARNAVAT VGAALPAFEV PRDASALNGT VNGDSVLQGV AEDA

UniProtKB: Probable amino acid decarboxylase

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Macromolecule #2: PYRIDOXAL-5'-PHOSPHATE

MacromoleculeName: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: PLP
Molecular weightTheoretical: 247.142 Da
Chemical component information

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

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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

Concentration0.6 mg/mL
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 / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000
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: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 379820
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: The intial model consists of the monomeric Rv2531c
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9n0o:
CryoEM structure of Rv2531c dimer from Mycobacterium tuberculosis

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