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- EMDB-53317: CryoEM structure of the tetrahedral M42 aminopeptidase from M. ja... -

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Basic information

Entry
Database: EMDB / ID: EMD-53317
TitleCryoEM structure of the tetrahedral M42 aminopeptidase from M. jannaschii
Map dataCryoEM map fro TET enzyme from Methanocaldococcus janaschii obtained using data collected with a Talos Glacios microscope and reconstructed using Relion.
Sample
  • Cell: MjTET
    • Protein or peptide: Putative aminopeptidase MJ0555
KeywordsEnzyme / aminopepidase / archaea / dodecamer / M42 / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42
Similarity search - Domain/homology
Putative aminopeptidase MJ0555
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsAtalah J / Basbous H / Girard E / Effantin E / Schoehn G / Franzetti B
Funding support France, 1 items
OrganizationGrant numberCountry
Grenoble Alliance for Integrated Structural Cell Biology (GRAL) France
CitationJournal: J Mol Biol / Year: 2026
Title: Structural and Biochemical Insights into the Broad-Spectrum TET Enzyme From Methanocaldococcus jannaschii Reveal the Basis of Substrate Specificity in M42 Aminopeptidases.
Authors: Joaquin Atalah / Hind Basbous / Gregory Effantin / Sylvie Kieffer-Jaquinod / Guy Schoehn / Eric Girard / Bruno Franzetti /
Abstract: TET peptidases of the M42 family are ∼500 kDa hollow dodecameric complexes ubiquitous in prokaryotes. These enzymes act as strict aminopeptidases, catalyzing the removal of N-terminal amino acids ...TET peptidases of the M42 family are ∼500 kDa hollow dodecameric complexes ubiquitous in prokaryotes. These enzymes act as strict aminopeptidases, catalyzing the removal of N-terminal amino acids from peptides. A common feature of M42 TET aminopeptidases characterized to date is their marked substrate preference for a limited subset of amino acids. Unlike other hyperthermophilic archaea studied so far, the autotrophic archaeon Methanocaldococcus jannaschii possesses only a single gene encoding an M42 peptidase. This enzyme, named MjTET, is the first reported M42 peptidase to exhibit broad amino acid specificity, including activity on aromatic residues. To assess their peptide degradation efficiencies, the catalytic constants of MjTET were compared to those of its close analogs from Pyrococcus horikoshii. The specialized TETs from P. horikoshii displayed higher catalytic efficiencies than the generalist MjTET, likely reflecting the reliance of Thermococcales on peptide fermentation for energy. Additionally, the structure of MjTET was resolved to 3 Å using cryo-EM and compared with the available models of the four P. horikoshii TETs to identify features underlying substrate specificity. This analysis, combined with mutagenesis studies, revealed a previously uncharacterized loop in the catalytic domain that contributes to substrate discrimination. Collectively, these findings show that substrate specificity in TET enzymes arises from a complex interplay of tertiary structure, oligomeric assembly, and electrostatic surface potential. IMPORTANCE: This study first reported a novel TET peptidase from Methanogenic hyperthermophilic archaea. Its enzymatic properties compared to the specialized TET enzyme characterized so far from heterotrophic archaea suggest a link with autotrophy. It also represents an important step in explaining the structural features guiding substrate specificity.
History
DepositionApr 3, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53317.png

Downloads & links

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Map

FileDownload / File: emd_53317.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map fro TET enzyme from Methanocaldococcus janaschii obtained using data collected with a Talos Glacios microscope and reconstructed using Relion.
Voxel sizeX=Y=Z: 0.915 Å
Density
Contour LevelBy AUTHOR: 0.0451
Minimum - Maximum-0.07890198 - 0.12760946
Average (Standard dev.)0.001573201 (±0.0090089645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 183.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53317_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53317_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MjTET

EntireName: MjTET
Components
  • Cell: MjTET
    • Protein or peptide: Putative aminopeptidase MJ0555

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Supramolecule #1: MjTET

SupramoleculeName: MjTET / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Enzyme obtained from genetically modified E. coli cells.
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)

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Macromolecule #1: Putative aminopeptidase MJ0555

MacromoleculeName: Putative aminopeptidase MJ0555 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Molecular weightTheoretical: 38.677625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVVEYLKKL SKLHGISGRE DSVREFMKKE LEKYCDSVEI DNFGNLIAKR GNKGKKIMIA AHMDEIGLMV KYIDDNGFLK FTKIGGIYD PTILNQKVVV HGSKGDLIGV LGSKPPHRMK EEEKTKIIKY EDMFIDIGAE SREEAIEMGV NIGTWVSFLS E VYDLGKNR ...String:
MSVVEYLKKL SKLHGISGRE DSVREFMKKE LEKYCDSVEI DNFGNLIAKR GNKGKKIMIA AHMDEIGLMV KYIDDNGFLK FTKIGGIYD PTILNQKVVV HGSKGDLIGV LGSKPPHRMK EEEKTKIIKY EDMFIDIGAE SREEAIEMGV NIGTWVSFLS E VYDLGKNR LTGKAFDDRV GCAVLLEVMK RLSEEDIDCQ VYAVGTVQEE VGLKGARVSA FKINPDVAIA LDVTIAGDHP GI KKEDAPV DLGKGPVVGI VDASGRGLIA HPKVLDMIKA VSEKYKIDVQ WEVGEGGTTD ATAIHLTREG IPTGVISVPA RYI HTPVEV IDKRDLEKTV ELVYNCIKEV NNFF

UniProtKB: Putative aminopeptidase MJ0555

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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 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsDetails: Low electron dose was applied
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 4.0 sec. / Average electron dose: 40.0 e/Å2 / Details: 40 frames
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Details: Angle assignment type: Euler

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Atomic model buiding 1

DetailsInitial fitting was done using Phenix.doc_in_map; consecutive refinement was done alternating automatic refinement in Phenix with manual refinement in coot.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qr6:
CryoEM structure of the tetrahedral M42 aminopeptidase from M. jannaschii

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