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- EMDB-52197: MnmE-MnmG a2b2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-52197
TitleMnmE-MnmG a2b2 complex
Map data
Sample
  • Complex: MnmE-MnmG complex
    • Protein or peptide: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
  • Protein or peptide: tRNA modification GTPase MnmE
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordstRNA modification / FAD binding protein / folate binding protein / G protein activated by dimerization / RNA BINDING PROTEIN
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
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA modification GTPase MnmE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsMaes L / Galicia C / Fislage M / Versees W
Funding support Belgium, 1 items
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, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52197.png

Downloads & links

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Map

FileDownload / File: emd_52197.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.76 Å/pix.
x 512 pix.
= 388.915 Å		0.76 Å/pix.
x 512 pix.
= 388.915 Å		0.76 Å/pix.
x 512 pix.
= 388.915 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7596 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-53.268203999999997 - 77.264859999999999
Average (Standard dev.)0.000000000000038 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 388.9152 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52197_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_52197_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 : MnmE-MnmG complex

EntireName: MnmE-MnmG complex
Components
  • Complex: MnmE-MnmG complex
    • Protein or peptide: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
  • Protein or peptide: tRNA modification GTPase MnmE
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: MnmE-MnmG complex

SupramoleculeName: MnmE-MnmG complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: tRNA modification GTPase MnmE

MacromoleculeName: tRNA modification GTPase MnmE / type: protein_or_peptide / ID: 1 / Details: MnmE bound to GTP analogue / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 49.286699 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP FKDADGSVLD QGIALWFPGP NSFTGEDVLE LQGHGGPVI LDLLLKRILT IPGLRIARPG EFSERAFLND KLDLAQAEAI ADLIDASSEQ AARSALNSLQ GAFSARVNHL V EALTHLRI ...String:
MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP FKDADGSVLD QGIALWFPGP NSFTGEDVLE LQGHGGPVI LDLLLKRILT IPGLRIARPG EFSERAFLND KLDLAQAEAI ADLIDASSEQ AARSALNSLQ GAFSARVNHL V EALTHLRI YVEAAIDFPD EEIDFLSDGK IEAQLNDVIA DLDAVRAEAR QGSLLREGMK VVIAGRPNAG KSSLLNALAG RE AAIVTDI AGTTRDVLRE HIHIDGMPLH IIDTAGLREA SDEVERIGIE RAWQEIEQAD RVLFMVDGTT TDAVDPAEIW PEF IARLPA KLPITVVRNK ADITGETLGM SEVNGHALIR LSARTGEGVD VLRNHLKQSM GFDTNMEGGF LARRRHLQAL EQAA EHLQQ GKAQLLGAWA GELLAEELRL AQQNLSEITG EFTSDDLLGR IFSSFCIGK

UniProtKB: tRNA modification GTPase MnmE

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Macromolecule #2: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG

MacromoleculeName: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
type: protein_or_peptide / ID: 2 / Details: MnmG bound to FAD / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 71.8775 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SSGENLYFQG MFYPDPFDVI IIGGGHAGTE AAMAAARMGQ QTLLLTHNID TLGQMSCNPA IGGIGKGHLV KEVDALGGL MAKAIDQAGI QFRILNASKG PAVRATRAQA DRVLYRQAVR TALENQPNLM IFQQAVEDLI VENDRVVGAV T QMGLKFRA ...String:
MGSSHHHHHH SSGENLYFQG MFYPDPFDVI IIGGGHAGTE AAMAAARMGQ QTLLLTHNID TLGQMSCNPA IGGIGKGHLV KEVDALGGL MAKAIDQAGI QFRILNASKG PAVRATRAQA DRVLYRQAVR TALENQPNLM IFQQAVEDLI VENDRVVGAV T QMGLKFRA KAVVLTVGTF LDGKIHIGLD NYSGGRAGDP PSIPLSRRLR ELPLRVGRLK TGTPPRIDAR TIDFSVLAQQ HG DNPMPVF SFMGNASQHP QQVPCYITHT NEKTHDVIRS NLDRSPMYAG VIEGVGPRYC PSIEDKVMRF ADRNQHQIFL EPE GLTSNE IYPNGISTSL PFDVQMQIVR SMQGMENAKI VRPGYAIEYD FFDPRDLKPT LESKFIQGLF FAGQINGTTG YEEA AAQGL LAGLNAARLS ADKEGWAPAR SQAYLGVLVD DLCTLGTKEP YRMFTSRAEY RLMLREDNAD LRLTEIGREL GLVDD ERWA RFNEKLENIE RERQRLKSTW VTPSAEAAAE VNAHLTAPLS REASGEDLLR RPEMTYEKLT TLTPFAPALT DEQAAE QVE IQVKYEGYIA RQQDEIEKQL RNENTLLPAT LDYRQVSGLS NEVIAKLNDH KPASIGQASR ISGVTPAAIS ILLVWLK KQ GMLRRSA

UniProtKB: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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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

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.55 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 116023
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9hip:
MnmE-MnmG a2b2 complex

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