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- PDB-9os7: Mycoplasma penetrans Methionyl tRNA Synthetase is an Asymmetric D... -

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Basic information

Entry
Database: PDB / ID: 9os7
TitleMycoplasma penetrans Methionyl tRNA Synthetase is an Asymmetric Dimer fused to N-terminal Ancillary Domains
Components(Methionine--tRNA ligase) x 2
KeywordsLIGASE / Methionine / tRNA transferase / Mycoplasma pentrans / graphene
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Methionine-tRNA synthetase, type 2 / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminotransferase class V domain / Aminotransferase class-V / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site ...Methionine-tRNA synthetase, type 2 / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminotransferase class V domain / Aminotransferase class-V / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Methionine--tRNA ligase
Similarity search - Component
Biological speciesMalacoplasma penetrans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsGhazi Esfahani, B. / Bowman, M. / Alexander, R. / Stroupe, M.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1856502 United States
National Science Foundation (NSF, United States)CHE1904612 United States
CitationJournal: PLoS One / Year: 2026
Title: Mycoplasma penetrans methionyl-tRNA synthetase dimerizes via tandem N-terminal ancillary domains.
Authors: Behrouz Ghazi Esfahani / Madelynn K Bowman / Nidhi Walia / Rebecca W Alexander / M Elizabeth Stroupe /
Abstract: Diverse aminoacyl-tRNA synthetase gene fusions are now recognized as a common mechanism for enhancing genetic diversity across all domains of life. The metS gene from Mycoplasma penetrans is a ...Diverse aminoacyl-tRNA synthetase gene fusions are now recognized as a common mechanism for enhancing genetic diversity across all domains of life. The metS gene from Mycoplasma penetrans is a striking example of such an evolutionary mechanism because although M. penetrans has a condensed genome, the metS gene is nearly twice the size of a typical bacterial gene encoding methionyl-tRNA synthetase (MetRS). We used cryo-EM to analyze the structure of the metS gene product (MpMetRS) to show that it is the fusion of three distinct enzyme domains: an N-terminal domain of unknown function, a dimeric alanine-glyoxylate aminotransferase (AGAT), and a MetRS. Only the first two N-terminal domains show two-fold symmetry and were resolved to 3.27 Å resolution; the MetRS domain is only partially resolved to 3.66 Å resolution. Modelling the full structure shows that a rotation of the MetRS domain relative to the AGAT domain must occur to accommodate a tRNA-bound MetRS. Further rearrangement of the catalytic domains would also be necessary to bring the active sites adjacent to one another if this unique assembly of catalytic domains functions to channel substrates to MetRS.
History
DepositionMay 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine--tRNA ligase
B: Methionine--tRNA ligase
C: Methionine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)186,8243
Polymers186,8243
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Only one c-termini domain is resolved.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 63656.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malacoplasma penetrans (bacteria) / Gene: metG, MYPE9380 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EUI8, methionine-tRNA ligase
#2: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 59510.004 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 582-1087)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malacoplasma penetrans (bacteria) / Gene: metG, MYPE9380 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EUI8, methionine-tRNA ligase
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mycoplasma penetrans methionyl tRNA synthetase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Malacoplasma penetrans (bacteria)
Source (recombinant)Organism: Ecoli xl10gold
Buffer solutionpH: 7.8
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.6particle selectionblob picker
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60101 / Symmetry type: POINT

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