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- PDB-9qqt: Methyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens... -

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Basic information

Entry
Database: PDB / ID: 9qqt
TitleMethyl-coenzyme M reductase of ANME-2d Candidatus Methanoperedens Vercelli Strain 1 from a bioreactor enrichment culture
Components(Methyl-coenzyme M reductase subunit ...) x 4
KeywordsTRANSFERASE / methanotrophy / anaerobic methanotrophic archaea / methane oxidation / methyl-coenzyme M reductase / ANME / MCR / reverse methanogenesis / nickel-dependent enzyme / coenzyme M / coenzyme B / F430 cofactor / post-translational modification
Function / homology
Function and homology information


coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding
Similarity search - Function
Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain / Methyl-coenzyme M reductase, alpha subunit, N-terminal / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, ferredoxin-like fold ...Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain / Methyl-coenzyme M reductase, alpha subunit, N-terminal / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, ferredoxin-like fold / Methyl-coenzyme M reductase, alpha subunit, C-terminal / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2 / Methyl-coenzyme M reductase alpha subunit, C-terminal domain / Methyl-coenzyme M reductase alpha subunit, N-terminal domain
Similarity search - Domain/homology
1-THIOETHANESULFONIC ACID / FACTOR 430 / : / Chem-SHT / Coenzyme B / Methyl-coenzyme M reductase subunit alpha / Methyl-coenzyme M reductase subunit beta
Similarity search - Component
Biological speciesCandidatus Methanoperedens sp. (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsMueller, M.-C. / Wagner, T.
Funding supportEuropean Union, Germany, Netherlands, 5items
OrganizationGrant numberCountry
European Research Council (ERC)101125699European Union
German Research Foundation (DFG)WA 4053/1-1 Germany
Netherlands Organisation for Scientific Research (NWO)VI.Vidi.223.012 Netherlands
Netherlands Organisation for Scientific Research (NWO)024.002.002 Netherlands
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2025
Title: Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications.
Authors: Muller, M.C. / Wissink, M. / Mukherjee, P. / Von Possel, N. / Laso-Perez, R. / Engilberge, S. / Carpentier, P. / Kahnt, J. / Wegener, G. / Welte, C.U. / Wagner, T.
History
DepositionApr 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-coenzyme M reductase subunit alpha
B: Methyl-coenzyme M reductase subunit beta
C: Methyl-coenzyme M reductase subunit gamma
D: Methyl-coenzyme M reductase subunit alpha
E: Methyl-coenzyme M reductase subunit beta
F: Methyl-coenzyme M reductase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,06037
Polymers270,9096
Non-polymers5,15231
Water59,3233293
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: All Methyl-CoM reductases so far have been characterised as dimers of heterotrimers.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.621, 189.823, 83.930
Angle α, β, γ (deg.)90.00, 114.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Methyl-coenzyme M reductase subunit ... , 4 types, 6 molecules ABECFD

#1: Protein Methyl-coenzyme M reductase subunit alpha


Mass: 61873.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The subunit alpha contains six post-translational modifications: Methylhistidine 272, Methylarginine 286, Hydroxytryptophane 443, Thioglycine 461, Didehydroaspartate 466, and Methylcysteine 468
Source: (natural) Candidatus Methanoperedens sp. (archaea) / Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: Vercelli strain 1 / Tissue: /
References: UniProt: A0A822J3V5, coenzyme-B sulfoethylthiotransferase
#2: Protein Methyl-coenzyme M reductase subunit beta / Coenzyme-B sulfoethylthiotransferase beta


Mass: 45334.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Candidatus Methanoperedens sp. (archaea) / Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: Vercelli strain 1 / Tissue: /
References: UniProt: A0A822J4Y5, coenzyme-B sulfoethylthiotransferase
#3: Protein Methyl-coenzyme M reductase subunit gamma


Mass: 28253.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The subunit gamma contains a methylhistidine at position 159
Source: (natural) Candidatus Methanoperedens sp. (archaea) / Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: Vercelli strain 1 / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#4: Protein Methyl-coenzyme M reductase subunit alpha


Mass: 61857.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The subunit alpha contains six post-translational modifications: Methylhistidine 272, Methylarginine 286, Hydroxytryptophane 443, Thioglycine 461, Didehydroaspartate 466, and Methylcysteine 468
Source: (natural) Candidatus Methanoperedens sp. (archaea) / Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: Vercelli strain 1 / Tissue: /
References: UniProt: A0A822J3V5, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 7 types, 3324 molecules

#5: Chemical ChemComp-K / POTASSIUM ION / Alpha subunit of the Methyl-coenzyme M reductase


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C42H51N6NiO13 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO7PS / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-SHT / O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE


Mass: 481.499 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C13H24NO10PS3 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3293 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.88 % / Description: Thick yellow brick-shaped
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: Crystals were produced on a Junior Clover plate using a crystallization solution containing 20 % w/v polyethylene glycol 3,350 and 200 mM sodium thiocyanate pH 6.9. The reservoir contained ...Details: Crystals were produced on a Junior Clover plate using a crystallization solution containing 20 % w/v polyethylene glycol 3,350 and 200 mM sodium thiocyanate pH 6.9. The reservoir contained 100 ul crystallization solution and drops of 2 ul solution were mixed with 3 ul protein at a concentration of 40 mg/ml in 25 mM Tris/HCl pH 8.0, 10% v/v glycerol, 100 mM NaCl and 2 mM dithiothreitol. Crystals were soaked in the crystallization solution containing 20 % v/v ethylene glycol before freezing in liquid nitrogen.
Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 0.977→94.911 Å / Num. obs: 996827 / % possible obs: 83.9 % / Redundancy: 7.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.03 / Rrim(I) all: 0.085 / Net I/σ(I): 13
Reflection shellResolution: 0.977→1.035 Å / Redundancy: 7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 49841 / CC1/2: 0.754 / Rpim(I) all: 0.32 / Rrim(I) all: 0.863 / % possible all: 62.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→41.71 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1481 49522 5.01 %
Rwork0.1283 --
obs0.1293 988480 74.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.98→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18922 0 325 3293 22540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01120525
X-RAY DIFFRACTIONf_angle_d1.38227986
X-RAY DIFFRACTIONf_dihedral_angle_d13.9417755
X-RAY DIFFRACTIONf_chiral_restr0.0963069
X-RAY DIFFRACTIONf_plane_restr0.0153678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.990.26921280.24282464X-RAY DIFFRACTION6
0.99-10.24233110.2226356X-RAY DIFFRACTION15
1-1.010.23034890.22139615X-RAY DIFFRACTION23
1.01-1.020.23137610.210314037X-RAY DIFFRACTION33
1.02-1.040.245110590.208819282X-RAY DIFFRACTION46
1.04-1.050.233715190.212228020X-RAY DIFFRACTION67
1.05-1.070.222717780.203632822X-RAY DIFFRACTION78
1.07-1.080.22318230.202834341X-RAY DIFFRACTION81
1.08-1.10.221518050.196134588X-RAY DIFFRACTION82
1.1-1.120.219717790.192134519X-RAY DIFFRACTION81
1.12-1.140.219318070.190133829X-RAY DIFFRACTION80
1.14-1.160.20616660.188331088X-RAY DIFFRACTION74
1.16-1.180.203418160.184635552X-RAY DIFFRACTION84
1.18-1.20.203519110.178635965X-RAY DIFFRACTION85
1.2-1.230.203818880.173135968X-RAY DIFFRACTION85
1.23-1.260.196619230.170135752X-RAY DIFFRACTION85
1.26-1.290.18419140.160135879X-RAY DIFFRACTION85
1.29-1.330.188317160.152435466X-RAY DIFFRACTION84
1.33-1.370.172617090.146932966X-RAY DIFFRACTION78
1.37-1.410.167418860.137535536X-RAY DIFFRACTION84
1.41-1.460.158420060.128837455X-RAY DIFFRACTION89
1.46-1.520.145320040.115837399X-RAY DIFFRACTION88
1.52-1.590.133719220.106237224X-RAY DIFFRACTION88
1.59-1.670.127719670.101436968X-RAY DIFFRACTION87
1.67-1.780.12618520.100336032X-RAY DIFFRACTION85
1.78-1.910.114718050.099934578X-RAY DIFFRACTION82
1.91-2.110.112521970.094438883X-RAY DIFFRACTION92
2.11-2.410.105621250.09138985X-RAY DIFFRACTION92
2.41-3.040.117419710.101338004X-RAY DIFFRACTION90
3.04-41.710.118219850.112239385X-RAY DIFFRACTION92

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