MCRA_METBF
ID MCRA_METBF Reviewed; 570 AA.
AC P07962; Q46E25;
DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=Methyl-coenzyme M reductase subunit alpha;
DE EC=2.8.4.1 {ECO:0000250|UniProtKB:P11558};
DE AltName: Full=Coenzyme-B sulfoethylthiotransferase alpha;
GN Name=mcrA; OrderedLocusNames=Mbar_A0893;
OS Methanosarcina barkeri (strain Fusaro / DSM 804).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=269797;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3502709; DOI=10.1093/nar/15.10.4350;
RA Bokranz M., Klein A.;
RT "Nucleotide sequence of the methyl coenzyme M reductase gene cluster from
RT Methanosarcina barkeri.";
RL Nucleic Acids Res. 15:4350-4351(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Fusaro / DSM 804;
RX PubMed=16980466; DOI=10.1128/jb.00810-06;
RA Maeder D.L., Anderson I., Brettin T.S., Bruce D.C., Gilna P., Han C.S.,
RA Lapidus A., Metcalf W.W., Saunders E., Tapia R., Sowers K.R.;
RT "The Methanosarcina barkeri genome: comparative analysis with
RT Methanosarcina acetivorans and Methanosarcina mazei reveals extensive
RT rearrangement within methanosarcinal genomes.";
RL J. Bacteriol. 188:7922-7931(2006).
RN [3]
RP METHYLATION AT CYS-472, THIOCARBOXYLATION AT GLY-465, AND DEHYDROGENATION
RP AT ASP-470.
RC STRAIN=Fusaro / DSM 804;
RX PubMed=27467699; DOI=10.1002/anie.201603882;
RA Wagner T., Kahnt J., Ermler U., Shima S.;
RT "Didehydroaspartate Modification in Methyl-CoenzymeM Reductase Catalyzing
RT Methane Formation.";
RL Angew. Chem. Int. Ed. Engl. 55:10630-10633(2016).
RN [4] {ECO:0007744|PDB:1E6Y}
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH COENZYME F430;
RP COENZYME B; COENZYME M AND MCR SUBUNITS BETA AND GAMMA, FUNCTION, COFACTOR,
RP METHYLATION AT HIS-271; ARG-285 AND CYS-472, THIOCARBOXYLATION AT GLY-465,
RP AND SUBUNIT.
RC STRAIN=Fusaro / DSM 804;
RX PubMed=11023796; DOI=10.1006/jmbi.2000.4136;
RA Grabarse W., Mahlert F., Shima S., Thauer R.K., Ermler U.;
RT "Comparison of three methyl-coenzyme M reductases from phylogenetically
RT distant organisms: unusual amino acid modification, conservation and
RT adaptation.";
RL J. Mol. Biol. 303:329-344(2000).
CC -!- FUNCTION: Component of the methyl-coenzyme M reductase (MCR) I that
CC catalyzes the reductive cleavage of methyl-coenzyme M (CoM-S-CH3 or 2-
CC (methylthio)ethanesulfonate) using coenzyme B (CoB or 7-
CC mercaptoheptanoylthreonine phosphate) as reductant which results in the
CC production of methane and the mixed heterodisulfide of CoB and CoM
CC (CoM-S-S-CoB). This is the final step in methanogenesis.
CC {ECO:0000305|PubMed:11023796}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=coenzyme B + methyl-coenzyme M = coenzyme M-coenzyme B
CC heterodisulfide + methane; Xref=Rhea:RHEA:12532, ChEBI:CHEBI:16183,
CC ChEBI:CHEBI:58286, ChEBI:CHEBI:58411, ChEBI:CHEBI:58596; EC=2.8.4.1;
CC Evidence={ECO:0000250|UniProtKB:P11558};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:12533;
CC Evidence={ECO:0000250|UniProtKB:P11558};
CC -!- COFACTOR:
CC Name=coenzyme F430; Xref=ChEBI:CHEBI:60540;
CC Evidence={ECO:0000269|PubMed:11023796};
CC Note=Binds 2 coenzyme F430 non-covalently per MCR complex. Coenzyme
CC F430 is a yellow nickel porphinoid (PubMed:11023796). Methyl-coenzyme-M
CC reductase is activated when the enzyme-bound coenzyme F430 is reduced
CC to the Ni(I) oxidation state (By similarity).
CC {ECO:0000250|UniProtKB:P11558, ECO:0000269|PubMed:11023796};
CC -!- PATHWAY: One-carbon metabolism; methyl-coenzyme M reduction; methane
CC from methyl-coenzyme M: step 1/1. {ECO:0000250|UniProtKB:P11558}.
CC -!- SUBUNIT: MCR is a hexamer of two alpha, two beta, and two gamma chains,
CC forming a dimer of heterotrimers. {ECO:0000269|PubMed:11023796}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P11558}.
CC -!- PTM: The alpha subunit contains five modified amino acids near the
CC active site region (PubMed:27467699, PubMed:11023796). Is methylated on
CC His-271, Arg-285 and Cys-472, probably by the action of specific S-
CC adenosylmethionine-dependent methyltransferases. Also contains a
CC thioglycine at position 465, forming a thiopeptide bond
CC (PubMed:27467699, PubMed:11023796). Contains a didehydroaspartate
CC residue at position 470 (PubMed:27467699). The methylation on C5 of
CC Arg-285 is a post-translational methylation not essential in vivo, but
CC which plays a role for the stability and structural integrity of MCR
CC (By similarity). Does not show a methylation at Gln-420, as shown for
CC M.marburgensis (PubMed:11023796). {ECO:0000250|UniProtKB:Q8THH1,
CC ECO:0000269|PubMed:11023796, ECO:0000269|PubMed:27467699}.
CC -!- SIMILARITY: Belongs to the methyl-coenzyme M reductase alpha subunit
CC family. {ECO:0000305}.
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DR EMBL; Y00158; CAA68357.1; -; Genomic_DNA.
DR EMBL; CP000099; AAZ69867.1; -; Genomic_DNA.
DR PIR; E29525; E29525.
DR RefSeq; WP_011305916.1; NC_007355.1.
DR PDB; 1E6Y; X-ray; 1.60 A; A/D=2-570.
DR PDBsum; 1E6Y; -.
DR AlphaFoldDB; P07962; -.
DR SMR; P07962; -.
DR STRING; 269797.Mbar_A0893; -.
DR iPTMnet; P07962; -.
DR PRIDE; P07962; -.
DR EnsemblBacteria; AAZ69867; AAZ69867; Mbar_A0893.
DR GeneID; 3625938; -.
DR KEGG; mba:Mbar_A0893; -.
DR eggNOG; arCOG04857; Archaea.
DR HOGENOM; CLU_493170_0_0_2; -.
DR OMA; AMLYDQI; -.
DR OrthoDB; 6589at2157; -.
DR BRENDA; 2.8.4.1; 3250.
DR UniPathway; UPA00646; UER00699.
DR EvolutionaryTrace; P07962; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0050524; F:coenzyme-B sulfoethylthiotransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0015948; P:methanogenesis; IEA:UniProtKB-KW.
DR Gene3D; 1.20.840.10; -; 1.
DR Gene3D; 3.30.70.470; -; 1.
DR Gene3D; 3.90.390.10; -; 1.
DR InterPro; IPR016212; Me_CoM_Rdtase_asu.
DR InterPro; IPR008924; Me_CoM_Rdtase_asu/bsu_C.
DR InterPro; IPR009047; Me_CoM_Rdtase_asu_C.
DR InterPro; IPR003183; Me_CoM_Rdtase_asu_N.
DR InterPro; IPR015811; Me_CoM_Rdtase_asu_N_sub1.
DR InterPro; IPR015823; Me_CoM_Rdtase_asu_N_sub2.
DR InterPro; IPR009024; Me_CoM_Rdtase_Fd-like_fold.
DR Pfam; PF02249; MCR_alpha; 1.
DR Pfam; PF02745; MCR_alpha_N; 1.
DR PIRSF; PIRSF000262; MCR_alpha; 1.
DR SUPFAM; SSF48081; SSF48081; 1.
DR SUPFAM; SSF55088; SSF55088; 1.
DR TIGRFAMs; TIGR03256; met_CoM_red_alp; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Metal-binding; Methanogenesis; Methylation;
KW Nickel; Transferase.
FT CHAIN 1..570
FT /note="Methyl-coenzyme M reductase subunit alpha"
FT /id="PRO_0000147449"
FT BINDING 161
FT /ligand="coenzyme F430"
FT /ligand_id="ChEBI:CHEBI:60540"
FT /ligand_part="Ni"
FT /ligand_part_id="ChEBI:CHEBI:28112"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:11023796,
FT ECO:0007744|PDB:1E6Y"
FT BINDING 239
FT /ligand="coenzyme B"
FT /ligand_id="ChEBI:CHEBI:58596"
FT /ligand_note="ligand shared between two alpha subunits"
FT /note="in chain A"
FT /evidence="ECO:0000269|PubMed:11023796,
FT ECO:0007744|PDB:1E6Y"
FT BINDING 270..271
FT /ligand="coenzyme B"
FT /ligand_id="ChEBI:CHEBI:58596"
FT /ligand_note="ligand shared between two alpha subunits"
FT /note="in chain A"
FT /evidence="ECO:0000269|PubMed:11023796,
FT ECO:0007744|PDB:1E6Y"
FT BINDING 284
FT /ligand="coenzyme B"
FT /ligand_id="ChEBI:CHEBI:58596"
FT /ligand_note="ligand shared between two alpha subunits"
FT /note="in chain B"
FT /evidence="ECO:0000269|PubMed:11023796,
FT ECO:0007744|PDB:1E6Y"
FT BINDING 346
FT /ligand="coenzyme M"
FT /ligand_id="ChEBI:CHEBI:58319"
FT /evidence="ECO:0000269|PubMed:11023796,
FT ECO:0007744|PDB:1E6Y"
FT BINDING 464
FT /ligand="coenzyme M"
FT /ligand_id="ChEBI:CHEBI:58319"
FT /evidence="ECO:0000269|PubMed:11023796,
FT ECO:0007744|PDB:1E6Y"
FT MOD_RES 271
FT /note="Pros-methylhistidine"
FT /evidence="ECO:0000269|PubMed:11023796"
FT MOD_RES 285
FT /note="5-methylarginine"
FT /evidence="ECO:0000269|PubMed:11023796"
FT MOD_RES 465
FT /note="1-thioglycine"
FT /evidence="ECO:0000269|PubMed:11023796,
FT ECO:0000269|PubMed:27467699"
FT MOD_RES 470
FT /note="(Z)-2,3-didehydroaspartate"
FT /evidence="ECO:0000269|PubMed:27467699"
FT MOD_RES 472
FT /note="S-methylcysteine"
FT /evidence="ECO:0000269|PubMed:11023796,
FT ECO:0000269|PubMed:27467699"
FT HELIX 3..17
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 47..63
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 70..72
FT /evidence="ECO:0007829|PDB:1E6Y"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:1E6Y"
FT STRAND 86..88
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 97..100
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 102..104
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 106..116
FT /evidence="ECO:0007829|PDB:1E6Y"
FT STRAND 118..123
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 124..134
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 140..153
FT /evidence="ECO:0007829|PDB:1E6Y"
FT TURN 154..156
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:1E6Y"
FT STRAND 176..182
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 184..187
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 192..194
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 198..201
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 204..214
FT /evidence="ECO:0007829|PDB:1E6Y"
FT STRAND 218..223
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 226..231
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 236..252
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 260..270
FT /evidence="ECO:0007829|PDB:1E6Y"
FT TURN 271..273
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 283..285
FT /evidence="ECO:0007829|PDB:1E6Y"
FT STRAND 289..291
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 292..294
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 297..303
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 306..309
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 313..330
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 331..336
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 344..348
FT /evidence="ECO:0007829|PDB:1E6Y"
FT TURN 349..351
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 355..370
FT /evidence="ECO:0007829|PDB:1E6Y"
FT STRAND 379..381
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 387..407
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 409..414
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 418..437
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 440..458
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 468..471
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 473..477
FT /evidence="ECO:0007829|PDB:1E6Y"
FT TURN 482..484
FT /evidence="ECO:0007829|PDB:1E6Y"
FT TURN 488..490
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 496..498
FT /evidence="ECO:0007829|PDB:1E6Y"
FT STRAND 502..504
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 505..517
FT /evidence="ECO:0007829|PDB:1E6Y"
FT TURN 518..520
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 527..532
FT /evidence="ECO:0007829|PDB:1E6Y"
FT STRAND 538..540
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 545..553
FT /evidence="ECO:0007829|PDB:1E6Y"
FT HELIX 564..566
FT /evidence="ECO:0007829|PDB:1E6Y"
SQ SEQUENCE 570 AA; 61962 MW; 301E10CE7D449C76 CRC64;
MAADIFSKFK KDMEVKFAQE FGSNKQTGGD ITDKTAKFLR LGPEQDPRKV EMIKAGKEIA
EKRGIAFYNP MMHSGAPLGQ RAITPYTISG TDIVCEPDDL HYVNNAAMQQ MWDDIRRTCI
VGLDMAHETL EKRLGKEVTP ETINHYLEVL NHAMPGAAVV QEMMVETHPA LVDDCYVKVF
TGDDALADEI DKQFLIDINK EFSEEQAAQI KASIGKTSWQ AIHIPTIVSR TTDGAQTSRW
AAMQIGMSFI SAYAMCAGEA AVADLSFAAK HAALVSMGEM LPARRARGPN EPGGLSFGHL
SDIVQTSRVS EDPAKIALEV VGAGCMLYDQ IWLGSYMSGG VGFTQYATAA YTDDILDNNT
YYDVDYINDK YNGAATVGKD NKVKASLEVV KDIATESTLY GIETYEKFPT ALEDHFGGSQ
RATVLAAAAG VACSLATGNA NAGLSGWYLS MYLHKEAWGR LGFFGFDLQD QCGATNVLSY
QGDEGLPDEL RGPNYPNYAM NVGHQGGYAG IAQAAHSGRG DAFTVNPLLK VCFADDLLPF
NFAEPRREFG RGAIREFVPA GERSLVIPAK
