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- PDB-9qts: Structure of the energy converting methyltransferase (Mtr) of Met... -

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Basic information

Entry
Database: PDB / ID: 9qts
TitleStructure of the energy converting methyltransferase (Mtr) of Methanosarcina mazei in complex with a novel protein binder
Components
  • (Tetrahydromethanopterin S-methyltransferase subunit ...) x 8
  • Conserved protein
KeywordsMEMBRANE PROTEIN / Sodium-pumping / membrane-bound / methyltransferase complex / methanogen / methanogenic / methylotrophic / archaeon / archaea / methanosarcina / methanosarcina mazei / Vitamin B12 / corrinoid / cobalt / 5-hydroxybenzimidazole / small protein / oxygen-sensitive
Function / homology
Function and homology information


tetrahydromethanopterin S-methyltransferase / tetrahydromethanopterin S-methyltransferase activity / methanogenesis, from carbon dioxide / vesicle membrane / cobalt ion binding / one-carbon metabolic process / methylation / plasma membrane / cytoplasm
Similarity search - Function
Tetrahydromethanopterin S-methyltransferase subunit H / Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase subunit B ...Tetrahydromethanopterin S-methyltransferase subunit H / Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase, subunit F / Tetrahydromethanopterin S-methyltransferase, F subunit / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF) / Tetrahydromethanopterin S-methyltransferase, subunit H/Methyltransferase Mtx, subunit H / Tetrahydromethanopterin S-methyltransferase MtrH subunit / Tetrahydromethanopterin S-methyltransferase subunit A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A / Dihydropteroate synthase-like
Similarity search - Domain/homology
: / : / : / 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / Tetrahydromethanopterin S-methyltransferase subunit C / Tetrahydromethanopterin S-methyltransferase subunit A / Tetrahydromethanopterin S-methyltransferase subunit H / Tetrahydromethanopterin S-methyltransferase subunit E / Tetrahydromethanopterin S-methyltransferase subunit D ...: / : / : / 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / Tetrahydromethanopterin S-methyltransferase subunit C / Tetrahydromethanopterin S-methyltransferase subunit A / Tetrahydromethanopterin S-methyltransferase subunit H / Tetrahydromethanopterin S-methyltransferase subunit E / Tetrahydromethanopterin S-methyltransferase subunit D / Tetrahydromethanopterin S-methyltransferase subunit F / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase subunit G / Conserved protein
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsReif-Trauttmansdorff, T. / Herdering, E. / Bohn, S. / Pascoa, T.C. / Kumar, A. / Zimmer, E. / Schmitz, R.A. / Schuller, J.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101075992European Union
CitationJournal: Nat Commun / Year: 2025
Title: Structure of the Methanosarcina mazei Mtr complex bound to the oxygen-stress responsive small protein MtrI.
Authors: Tristan Reif-Trauttmansdorff / Eva Herdering / Stefan Bohn / Tomas Pascoa / Jörg Kahnt / Erik Zimmer / Anuj Kumar / Ruth A Schmitz / Jan M Schuller /
Abstract: Methanogenic archaea emit ~1 Gt of methane annually, impacting global carbon cycling and climate. Central to their energy metabolism is a membrane-bound, sodium-translocating methyltransferase ...Methanogenic archaea emit ~1 Gt of methane annually, impacting global carbon cycling and climate. Central to their energy metabolism is a membrane-bound, sodium-translocating methyltransferase complex: the N⁵-tetrahydromethanopterin:CoM-S-methyltransferase (Mtr). It couples methyl transfer between two methanogen-specific cofactors with sodium ion transport across the membrane, forming the only energy-conserving step in hydrogenotrophic methanogenesis. Here, we present a 2.1 Å single-particle cryo-EM structure of the Mtr complex from Methanosarcina mazei. The structure reveals the organization of all catalytic subunits, embedded archaeal lipids and the sodium-binding site. Most strikingly, we discover MtrI, a previously unannotated small open-reading frame encoded protein ( < 100 aa) found within the order of Methanosarcinales that binds both the top of the sodium-channel and cytosolic domain of MtrA via its cobamide cofactor in response to oxygen exposure. This interaction likely prevents sodium leakage and stabilizes the complex under oxidative conditions, revealing an unexpected regulatory mechanism in methanogen energy conservation.
History
DepositionApr 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Jan 7, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _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: Tetrahydromethanopterin S-methyltransferase subunit A
B: Tetrahydromethanopterin S-methyltransferase subunit A
C: Tetrahydromethanopterin S-methyltransferase subunit A
D: Tetrahydromethanopterin S-methyltransferase subunit B
E: Tetrahydromethanopterin S-methyltransferase subunit B
F: Tetrahydromethanopterin S-methyltransferase subunit B
G: Tetrahydromethanopterin S-methyltransferase subunit C
H: Tetrahydromethanopterin S-methyltransferase subunit C
I: Tetrahydromethanopterin S-methyltransferase subunit C
J: Tetrahydromethanopterin S-methyltransferase subunit D
K: Tetrahydromethanopterin S-methyltransferase subunit D
L: Tetrahydromethanopterin S-methyltransferase subunit D
M: Tetrahydromethanopterin S-methyltransferase subunit E
N: Tetrahydromethanopterin S-methyltransferase subunit E
O: Tetrahydromethanopterin S-methyltransferase subunit E
P: Tetrahydromethanopterin S-methyltransferase subunit F
Q: Tetrahydromethanopterin S-methyltransferase subunit F
R: Tetrahydromethanopterin S-methyltransferase subunit F
S: Tetrahydromethanopterin S-methyltransferase subunit G
T: Tetrahydromethanopterin S-methyltransferase subunit G
U: Tetrahydromethanopterin S-methyltransferase subunit G
i: Conserved protein
m: Tetrahydromethanopterin S-methyltransferase subunit H
n: Tetrahydromethanopterin S-methyltransferase subunit H
o: Tetrahydromethanopterin S-methyltransferase subunit H
p: Tetrahydromethanopterin S-methyltransferase subunit H
q: Tetrahydromethanopterin S-methyltransferase subunit H
r: Tetrahydromethanopterin S-methyltransferase subunit H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)647,70547
Polymers634,03528
Non-polymers13,66919
Water47,5782641
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

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Tetrahydromethanopterin S-methyltransferase subunit ... , 8 types, 27 molecules ABCDEFGHIJKLMNOPQRSTUmnopqr

#1: Protein Tetrahydromethanopterin S-methyltransferase subunit A / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit A


Mass: 25395.191 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrA, MM_1543 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: O59640, tetrahydromethanopterin S-methyltransferase
#2: Protein Tetrahydromethanopterin S-methyltransferase subunit B / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit B


Mass: 11879.630 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrB, MM_1544 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80655, tetrahydromethanopterin S-methyltransferase
#3: Protein Tetrahydromethanopterin S-methyltransferase subunit C / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit C


Mass: 26953.893 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrC, MM_1545 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: O59638, tetrahydromethanopterin S-methyltransferase
#4: Protein Tetrahydromethanopterin S-methyltransferase subunit D / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit D


Mass: 25279.777 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrD, MM_1546 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80653, tetrahydromethanopterin S-methyltransferase
#5: Protein Tetrahydromethanopterin S-methyltransferase subunit E / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit E


Mass: 35539.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: c-terminal Twin-StrepTag / Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrE, MM_1547 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80651, tetrahydromethanopterin S-methyltransferase
#6: Protein Tetrahydromethanopterin S-methyltransferase subunit F / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit F


Mass: 7573.959 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrF, MM_1542 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80654, tetrahydromethanopterin S-methyltransferase
#7: Protein Tetrahydromethanopterin S-methyltransferase subunit G / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit G


Mass: 8030.405 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrG, MM_1541 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80656, tetrahydromethanopterin S-methyltransferase
#9: Protein
Tetrahydromethanopterin S-methyltransferase subunit H / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit H


Mass: 34075.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: mtrH, MM_1540 / Production host: Methanosarcina mazei Go1 (archaea)
References: UniProt: P80650, tetrahydromethanopterin S-methyltransferase

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Protein , 1 types, 1 molecules i

#8: Protein Conserved protein


Mass: 7623.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: MM_2401 / Production host: Methanosarcina mazei Go1 (archaea) / References: UniProt: Q8PUD4

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Non-polymers , 7 types, 2660 molecules

#10: Chemical ChemComp-B13 / 5-HYDROXYBENZIMIDAZOLYLCOB(III)AMIDE


Mass: 1321.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C60H88CoN13O15P / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-A1JAP / 2-Hydroxy-archaetidylinositol / (2~{S})-2-azanyl-3-[oxidanyl-[(2~{S})-3-[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethylhexadecoxy]-2-[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethyl-3-oxidanyl-hexadecoxy]propoxy]phosphoryl]oxy-propanoic acid


Mass: 836.214 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C46H94NO9P / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-L1P / 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCERO-3-PHOSPHATE


Mass: 733.137 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C43H89O6P / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-A1JAO / Archaetidylinositol / [(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl] [(2~{S})-3-[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethylhexadecoxy]-2-[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethyl-3-oxidanyl-hexadecoxy]propyl] hydrogen phosphate


Mass: 911.277 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C49H99O12P / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-A1JAN / Archaetidylethanolamine / 2-azanylethyl [(2~{S})-2,3-bis[(3~{R},7~{R},11~{R})-3,7,11,15-tetramethylhexadecoxy]propyl] hydrogen phosphate


Mass: 776.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H94NO6P / Feature type: SUBJECT OF INVESTIGATION
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2641 / Source method: isolated from a natural source / Formula: H2O

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Details

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: Mtr complex / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Buffer solutionpH: 7
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.06 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002242176
ELECTRON MICROSCOPYf_angle_d0.431457260
ELECTRON MICROSCOPYf_chiral_restr0.03866797
ELECTRON MICROSCOPYf_plane_restr0.00377144
ELECTRON MICROSCOPYf_dihedral_angle_d8.6336419

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