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- EMDB-70794: Mycoplasma penetrans Methionyl tRNA Synthetase is an Asymmetric D... -

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Basic information

Entry
Database: EMDB / ID: EMD-70794
TitleMycoplasma penetrans Methionyl tRNA Synthetase is an Asymmetric Dimer fused to N-terminal Ancillary Domains
Map data
Sample
  • Complex: Mycoplasma penetrans methionyl tRNA synthetase
    • Protein or peptide: Methionine--tRNA ligase
  • Protein or peptide: Methionine--tRNA ligase
KeywordsMethionine / tRNA transferase / Mycoplasma pentrans / graphene / LIGASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsGhazi Esfahani B / Bowman M / Alexander R / Stroupe ME
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70794.png

Downloads & links

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Map

FileDownload / File: emd_70794.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 420 pix.
= 361.2 Å		0.86 Å/pix.
x 420 pix.
= 361.2 Å		0.86 Å/pix.
x 420 pix.
= 361.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.3607612 - 2.3258984
Average (Standard dev.)-0.00014581523 (±0.035188787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 361.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70794_additional_1.map
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Additional map: #2

Fileemd_70794_additional_2.map
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Half map: #1

Fileemd_70794_half_map_1.map
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Half map: #2

Fileemd_70794_half_map_2.map
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Sample components

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Entire : Mycoplasma penetrans methionyl tRNA synthetase

EntireName: Mycoplasma penetrans methionyl tRNA synthetase
Components
  • Complex: Mycoplasma penetrans methionyl tRNA synthetase
    • Protein or peptide: Methionine--tRNA ligase
  • Protein or peptide: Methionine--tRNA ligase

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Supramolecule #1: Mycoplasma penetrans methionyl tRNA synthetase

SupramoleculeName: Mycoplasma penetrans methionyl tRNA synthetase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Malacoplasma penetrans (bacteria)

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Macromolecule #1: Methionine--tRNA ligase

MacromoleculeName: Methionine--tRNA ligase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: methionine-tRNA ligase
Source (natural)Organism: Malacoplasma penetrans (bacteria)
Molecular weightTheoretical: 63.656805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KYMNFNSVII NVNTSKKNKF ILNGFNLNGL FSINEKTIMD NNIELFSEAN LNVYIVIEKQ YSNILKKHLV NIEKVQILLK EDFFNQKNF IKSDEKTLIV DDNFYFNQEI LNNLLTNEKY SNLSTLIKLN YNTHFDYIGI FDSTSINYID FKNNSISDDI K VLSNLVEL ...String:
KYMNFNSVII NVNTSKKNKF ILNGFNLNGL FSINEKTIMD NNIELFSEAN LNVYIVIEKQ YSNILKKHLV NIEKVQILLK EDFFNQKNF IKSDEKTLIV DDNFYFNQEI LNNLLTNEKY SNLSTLIKLN YNTHFDYIGI FDSTSINYID FKNNSISDDI K VLSNLVEL KEKQYLPIKI YDYKTLSKMD SKYECDKGFL YFTPGPVQIR EWVKEVLGEY VNHHRSLSIK EIYKEAAENI KW AFNSKKG YPIAMANTGL GAIESTFVNL LEQGDEILIL SNGFFGENLI DIAKRHQLNQ SLLQIKQGES FDLKEVENLI KNK KAVFMV YMDTSCGILN PVKKVGELCK DYGCLFIVDA ISGILNEEFN FDEYGVTAAV STSGKGFEVS PGLAFVCVSE QGMQ ISANI KKRKPKFLDW QTFKVRSLYD GLTPSTYPVN IFASLNKVCE EIKDNGGLTR LIDKKFNLNL YLSESLITLG FRHII ENEN SRSNWVLVME TPNIIKANEL RAYLYAMKNI LIECGIADSS NRIVRLAISA AHDIEDVTQL IEAIKEYIDL K

UniProtKB: Methionine--tRNA ligase

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Macromolecule #2: Methionine--tRNA ligase

MacromoleculeName: Methionine--tRNA ligase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: methionine-tRNA ligase
Source (natural)Organism: Malacoplasma penetrans (bacteria)
Molecular weightTheoretical: 59.510004 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GNPHIGHAFT TLIADVLTRY KKKLGYETFF ITGMDEHGQK IEEKAKELNL KPQELVDKYA KVFDNLWKLL GIEYSHFIRT TAEYHKNVV QETFSELLKK DFIYLGVWKG LYCVSCEENY TKNIAVRKEN DDKLYCAQLH PLIQKEEESY FLKIKQFKKY I SSFLKDPN ...String:
GNPHIGHAFT TLIADVLTRY KKKLGYETFF ITGMDEHGQK IEEKAKELNL KPQELVDKYA KVFDNLWKLL GIEYSHFIRT TAEYHKNVV QETFSELLKK DFIYLGVWKG LYCVSCEENY TKNIAVRKEN DDKLYCAQLH PLIQKEEESY FLKIKQFKKY I SSFLKDPN LVYPITRINE LFNSFLNNDD FDDLSISRSN FSWGIQIKEN PKHVVYVWLD ALLNYLSGLG YRQKDDSNFQ KF WNSQDAE IVQLMSKEIG NPHIGHAFTT LIADVLRTRY KKKLHGWIIT EQGKMSKSLG NVLDPIYFIN TYGRDAFRYY LLK ELSLKE DSVFSEKLLI NTFNKDLANN VGNLFNRSIG MINKYRDGII PKYSKPKLSF NIEFEKQLKQ FDDEITTIIE KLNI QKILS RVIDLINECN FFIEQVKPWD LKKENNEKDL DCFLSLILNA VKRVIYYLEP VLIDGSKEAL KQFNIDSSKF DIKFV TDFS SLDNQKINTP EPIYLRIESE DK

UniProtKB: Methionine--tRNA ligase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k 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: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: Alphafold 3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60101
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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