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- PDB-9hip: MnmE-MnmG a2b2 complex -

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Basic information

Entry
Database: PDB / ID: 9hip
TitleMnmE-MnmG a2b2 complex
Components
  • tRNA modification GTPase MnmE
  • tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
KeywordsRNA BINDING PROTEIN / tRNA modification / FAD binding protein / folate binding protein / G protein activated by dimerization
Function / homology
Function and homology information


regulation of cytoplasmic translational fidelity / cytosolic tRNA wobble base thiouridylase complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Hydrolases; Acting on acid anhydrides / tRNA wobble uridine modification / tRNA methylation / response to pH / potassium ion binding / response to UV / : ...regulation of cytoplasmic translational fidelity / cytosolic tRNA wobble base thiouridylase complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Hydrolases; Acting on acid anhydrides / tRNA wobble uridine modification / tRNA methylation / response to pH / potassium ion binding / response to UV / : / GDP binding / flavin adenine dinucleotide binding / GTPase activity / GTP binding / protein homodimerization activity / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal ...tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal / tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain / : / : / tRNA modifying enzyme MnmG/GidA C-terminal helical bundle / tRNA modifying enzyme MnmG/GidA C-terminal helical domain / Glucose inhibited division protein A family signature 1. / GidA associated domain 3 / MnmG-related, conserved site / Glucose inhibited division protein A family signature 2. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related / MnmG, N-terminal domain / Glucose inhibited division protein A / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 50S ribosome-binding GTPase / GTP binding domain / FAD/NAD(P)-binding domain superfamily / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA modification GTPase MnmE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsMaes, L. / Galicia, C. / Fislage, M. / Versees, W.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Vrije Universiteit BrusselSRP95 Belgium
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification.
Authors: Laila Maes / Israel Mares-Mejía / Ella Martin / David Bickel / Siemen Claeys / Wim Vranken / Marcus Fislage / Christian Galicia / Wim Versées /
Abstract: MnmE and MnmG form a conserved protein complex responsible for the addition of a 5-carboxymethylaminomethyl (cmnm5) group onto the wobble uridine of several transfer RNAs (tRNAs). Within this ...MnmE and MnmG form a conserved protein complex responsible for the addition of a 5-carboxymethylaminomethyl (cmnm5) group onto the wobble uridine of several transfer RNAs (tRNAs). Within this complex, both proteins collaborate intensively to catalyze a tRNA modification reaction that involves glycine as a substrate in addition to three different cofactors, with FAD and NADH binding to MnmG and methylenetetrahydrofolate (5,10-CH2-THF) to MnmE. Without structures of the MnmEG complex, it remained enigmatic how these substrates and co-factors can be brought together in a concerted manner. Prior small angle X-ray scattering data suggested that the MnmE (α2) and MnmG (β2) homo-dimers can adopt either an α2β2 or α4β2 complex, depending on the nucleotide state of MnmE. Here, we report the cryo-EM structures of the MnmEG complex in the α2β2 and α4β2 oligomeric states. These structures reveal that MnmE undergoes large conformational changes upon interaction with MnmG, resulting in an asymmetric MnmE dimer. In particular, the functionally important C-terminal helix of MnmE relocates from the 5,10-CH2-THF-binding pocket of MnmE to the FAD-binding pocket of MnmG, thus suggesting a mechanism for the transfer of an activated methylene group from one active site to the other. Together, these findings provide crucial new insights into the MnmEG-catalyzed reaction.
History
DepositionNov 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Sep 17, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA modification GTPase MnmE
B: tRNA modification GTPase MnmE
C: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
D: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,1587
Polymers242,3284
Non-polymers1,8303
Water00
1


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

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Components

#1: Protein tRNA modification GTPase MnmE


Mass: 49286.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MnmE bound to GTP analogue / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mnmE, thdF, trmE, b3706, JW3684 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P25522, Hydrolases; Acting on acid anhydrides
#2: Protein tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / Glucose-inhibited division protein A


Mass: 71877.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MnmG bound to FAD / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mnmG, gidA, trmF, b3741, JW3719 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A6U3
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
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: MnmE-MnmG complex / Type: COMPLEX / Entity ID: #2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 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: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.55 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEM3.0.8image acquisition
12cryoSPARC4.6.03D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116023 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementHighest resolution: 3.31 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416095
ELECTRON MICROSCOPYf_angle_d0.55621823
ELECTRON MICROSCOPYf_dihedral_angle_d12.8516094
ELECTRON MICROSCOPYf_chiral_restr0.0372457
ELECTRON MICROSCOPYf_plane_restr0.0042887

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