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

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Basic information

Entry
Database: PDB / ID: 9qr6
TitleCryoEM structure of the tetrahedral M42 aminopeptidase from M. jannaschii
ComponentsPutative aminopeptidase MJ0555
KeywordsCYTOSOLIC PROTEIN / Enzyme / aminopepidase / archaea / dodecamer / M42
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsAtalah, J. / Basbous, H. / Girard, E. / Effantin, E. / Schoehn, G. / Franzetti, B.
Funding support France, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative aminopeptidase MJ0555
B: Putative aminopeptidase MJ0555
C: Putative aminopeptidase MJ0555
D: Putative aminopeptidase MJ0555
E: Putative aminopeptidase MJ0555
F: Putative aminopeptidase MJ0555
G: Putative aminopeptidase MJ0555
H: Putative aminopeptidase MJ0555
I: Putative aminopeptidase MJ0555
J: Putative aminopeptidase MJ0555
K: Putative aminopeptidase MJ0555
L: Putative aminopeptidase MJ0555


Theoretical massNumber of molelcules
Total (without water)464,13212
Polymers464,13212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Putative aminopeptidase MJ0555


Mass: 38677.625 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0555 / Production host: Escherichia coli (E. coli) / Strain (production host): Artic express (DE3)
References: UniProt: Q57975, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: MjTET / Type: CELL
Details: Enzyme obtained from genetically modified E. coli cells.
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Arctic Express (DE3)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Details: 40 frames
EM imaging opticsDetails: Low electron dose was applied

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial fitting was done using Phenix.doc_in_map; consecutive refinement was done alternating automatic refinement in Phenix with manual refinement in coot.
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00832636
ELECTRON MICROSCOPYf_angle_d0.58144015
ELECTRON MICROSCOPYf_dihedral_angle_d4.3064466
ELECTRON MICROSCOPYf_chiral_restr0.0485065
ELECTRON MICROSCOPYf_plane_restr0.0035647

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