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- PDB-8q3v: Cryo-EM structure of the methanogenic Na+ translocating N5-methyl... -

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Basic information

Entry
Database: PDB / ID: 8q3v
TitleCryo-EM structure of the methanogenic Na+ translocating N5-methyl-H4MPT:CoM methyltransferase complex
Components(Tetrahydromethanopterin S-methyltransferase subunit ...) x 7
KeywordsTRANSFERASE / methanogenesis / tetrahydromethanopterin / coenzyme M / vitamin B12 / Na+ transport
Function / homology
Function and homology information


tetrahydromethanopterin S-methyltransferase / tetrahydromethanopterin S-methyltransferase activity / methyltransferase complex / methanogenesis, from carbon dioxide / vesicle membrane / cobalt ion binding / one-carbon metabolic process / methylation / plasma membrane / cytoplasm
Similarity search - Function
Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase, subunit F / Tetrahydromethanopterin S-methyltransferase, F subunit / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit G ...Tetrahydromethanopterin S-methyltransferase, subunit D / Tetrahydromethanopterin S-methyltransferase, subunit E / Tetrahydromethanopterin S-methyltransferase, subunit C / Tetrahydromethanopterin S-methyltransferase, subunit G / Tetrahydromethanopterin S-methyltransferase subunit B / Tetrahydromethanopterin S-methyltransferase, subunit F / Tetrahydromethanopterin S-methyltransferase, F subunit / 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, F subunit (MtrF) / Tetrahydromethanopterin S-methyltransferase subunit A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A
Similarity search - Domain/homology
: / Tetrahydromethanopterin S-methyltransferase subunit D / Tetrahydromethanopterin S-methyltransferase subunit A 1 / Tetrahydromethanopterin S-methyltransferase subunit C / Tetrahydromethanopterin S-methyltransferase subunit E / Tetrahydromethanopterin S-methyltransferase subunit F / Tetrahydromethanopterin S-methyltransferase subunit G / Tetrahydromethanopterin S-methyltransferase subunit B
Similarity search - Component
Biological speciesMethanothermobacter marburgensis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsAziz, I. / Vonck, J. / Ermler, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alexander von Humboldt FoundationGeorg Forster stipend Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis.
Authors: Iram Aziz / Kanwal Kayastha / Susann Kaltwasser / Janet Vonck / Sonja Welsch / Bonnie J Murphy / Jörg Kahnt / Di Wu / Tristan Wagner / Seigo Shima / Ulrich Ermler /
Abstract: Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy ...Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy metabolism is catalyzed by -methyl-tetrahydromethanopterin: coenzyme M methyltransferase (MtrABCDEFGH), which couples the vectorial Na transport with a methyl transfer between the one-carbon carriers tetrahydromethanopterin and coenzyme M via a vitamin B derivative (cobamide) as prosthetic group. We present the 2.08 Å cryo-EM structure of Mtr(ABCDEFG) composed of the central Mtr(ABFG) stalk symmetrically flanked by three membrane-spanning MtrCDE globes. Tetraether glycolipids visible in the map fill gaps inside the multisubunit complex. Putative coenzyme M and Na were identified inside or in a side-pocket of a cytoplasmic cavity formed within MtrCDE. Its bottom marks the gate of the transmembrane pore occluded in the cryo-EM map. By integrating Alphafold2 information, functionally competent MtrA-MtrH and MtrA-MtrCDE subcomplexes could be modeled and thus the methyl-tetrahydromethanopterin demethylation and coenzyme M methylation half-reactions structurally described. Methyl-transfer-driven Na transport is proposed to be based on a strong and weak complex between MtrCDE and MtrA carrying vitamin B, the latter being placed at the entrance of the cytoplasmic MtrCDE cavity. Hypothetically, strongly attached methyl-cob(III)amide (His-on) carrying MtrA induces an inward-facing conformation, Na flux into the membrane protein center and finally coenzyme M methylation while the generated loosely attached (or detached) MtrA carrying cob(I)amide (His-off) induces an outward-facing conformation and an extracellular Na outflux. Methyl-cob(III)amide (His-on) is regenerated in the distant active site of the methyl-tetrahydromethanopterin binding MtrH implicating a large-scale shuttling movement of the vitamin B-carrying domain.
History
DepositionAug 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetrahydromethanopterin S-methyltransferase subunit A 1
B: Tetrahydromethanopterin S-methyltransferase subunit B
C: Tetrahydromethanopterin S-methyltransferase subunit C
D: Tetrahydromethanopterin S-methyltransferase subunit D
E: Tetrahydromethanopterin S-methyltransferase subunit E
F: Tetrahydromethanopterin S-methyltransferase subunit F
G: Tetrahydromethanopterin S-methyltransferase subunit G
a: Tetrahydromethanopterin S-methyltransferase subunit A 1
b: Tetrahydromethanopterin S-methyltransferase subunit B
c: Tetrahydromethanopterin S-methyltransferase subunit C
d: Tetrahydromethanopterin S-methyltransferase subunit D
e: Tetrahydromethanopterin S-methyltransferase subunit E
f: Tetrahydromethanopterin S-methyltransferase subunit F
g: Tetrahydromethanopterin S-methyltransferase subunit G
Q: Tetrahydromethanopterin S-methyltransferase subunit A 1
R: Tetrahydromethanopterin S-methyltransferase subunit B
S: Tetrahydromethanopterin S-methyltransferase subunit C
T: Tetrahydromethanopterin S-methyltransferase subunit D
U: Tetrahydromethanopterin S-methyltransferase subunit E
V: Tetrahydromethanopterin S-methyltransferase subunit F
W: Tetrahydromethanopterin S-methyltransferase subunit G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)423,83042
Polymers403,14121
Non-polymers20,68921
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area133130 Å2
ΔGint-1209 kcal/mol
Surface area74030 Å2
MethodPISA

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Components

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Tetrahydromethanopterin S-methyltransferase subunit ... , 7 types, 21 molecules AaQBbRCcSDdTEeUFfVGgW

#1: Protein Tetrahydromethanopterin S-methyltransferase subunit A 1


Mass: 25640.320 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P80184
#2: Protein Tetrahydromethanopterin S-methyltransferase subunit B


Mass: 10725.471 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q59584
#3: Protein Tetrahydromethanopterin S-methyltransferase subunit C


Mass: 27132.244 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P80185
#4: Protein Tetrahydromethanopterin S-methyltransferase subunit D


Mass: 22783.881 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P80183
#5: Protein Tetrahydromethanopterin S-methyltransferase subunit E


Mass: 31253.289 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: P80186
#6: Protein Tetrahydromethanopterin S-methyltransferase subunit F


Mass: 7325.928 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50773
#7: Protein Tetrahydromethanopterin S-methyltransferase subunit G


Mass: 9519.042 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis (archaea)
References: UniProt: Q50774

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Non-polymers , 4 types, 229 molecules

#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-JCV / [(2~{S},7~{R},11~{R},15~{S},19~{S},22~{S},26~{S},30~{R},34~{R},39~{S},43~{R},47~{R},51~{S},55~{S},58~{S},62~{S},66~{R},70~{R})-39-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-7,11,15,19,22,26,30,34,43,47,51,55,58,62,66,70-hexadecamethyl-1,4,37,40-tetraoxacyclodoheptacont-2-yl]methyl [(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl] hydrogen phosphate


Mass: 1706.543 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C98H193O19P
#10: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Methyl-H4MPT:CoM methyltransferase / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 430 kDa/nm / Experimental value: YES
Source (natural)Organism: Methanothermobacter marburgensis (archaea)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 73.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138464 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00524947
ELECTRON MICROSCOPYf_angle_d0.90833818
ELECTRON MICROSCOPYf_dihedral_angle_d15.763725
ELECTRON MICROSCOPYf_chiral_restr0.0344257
ELECTRON MICROSCOPYf_plane_restr0.0073995

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