MCRX_METTM
ID MCRX_METTM Reviewed; 553 AA.
AC P58815; D9PXZ3;
DT 10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 30-NOV-2010, sequence version 2.
DT 03-AUG-2022, entry version 79.
DE RecName: Full=Methyl-coenzyme M reductase II subunit alpha {ECO:0000303|PubMed:2269306};
DE Short=MCR II alpha {ECO:0000303|PubMed:2269306};
DE EC=2.8.4.1 {ECO:0000269|PubMed:2269306};
GN Name=mrtA; OrderedLocusNames=MTBMA_c15120;
OS Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM
OS 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium
OS thermoautotrophicum).
OC Archaea; Euryarchaeota; Methanomada group; Methanobacteria;
OC Methanobacteriales; Methanobacteriaceae; Methanothermobacter.
OX NCBI_TaxID=79929;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 /
RC Marburg;
RX PubMed=20802048; DOI=10.1128/jb.00844-10;
RA Liesegang H., Kaster A.K., Wiezer A., Goenrich M., Wollherr A., Seedorf H.,
RA Gottschalk G., Thauer R.K.;
RT "Complete genome sequence of Methanothermobacter marburgensis, a
RT methanoarchaeon model organism.";
RL J. Bacteriol. 192:5850-5851(2010).
RN [2]
RP PROTEIN SEQUENCE OF 1-14, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBUNIT, AND DEVELOPMENTAL STAGE.
RC STRAIN=ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 /
RC Marburg;
RX PubMed=2269306; DOI=10.1111/j.1432-1033.1990.tb19481.x;
RA Rospert S., Linder D., Ellermann J., Thauer R.K.;
RT "Two genetically distinct methyl-coenzyme M reductases in Methanobacterium
RT thermoautotrophicum strain Marburg and delta H.";
RL Eur. J. Biochem. 194:871-877(1990).
RN [3] {ECO:0007744|PDB:5A8R}
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEX WITH COENZYME F430;
RP COENZYME B; COENZYME M AND MCR SUBUNITS BETA AND GAMMA, COFACTOR,
RP METHYLATION AT HIS-260; ARG-274; GLN-402 AND CYS-454, THIOCARBOXYLATION AT
RP GLY-447, DEHYDROGENATION AT ASP-452, AND SUBUNIT.
RC STRAIN=ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 /
RC Marburg;
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).
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:0000269|PubMed:2269306}.
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:0000269|PubMed:2269306};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:12533;
CC Evidence={ECO:0000305|PubMed:2269306};
CC -!- COFACTOR:
CC Name=coenzyme F430; Xref=ChEBI:CHEBI:60540;
CC Evidence={ECO:0000269|PubMed:27467699};
CC Note=Binds 2 coenzyme F430 non-covalently per MCR complex. Coenzyme
CC F430 is a yellow nickel porphinoid (PubMed:27467699). 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:27467699};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=75 uM for coenzyme B {ECO:0000269|PubMed:2269306};
CC KM=4 mM for methyl-coenzyme M {ECO:0000269|PubMed:2269306};
CC -!- PATHWAY: One-carbon metabolism; methyl-coenzyme M reduction; methane
CC from methyl-coenzyme M: step 1/1. {ECO:0000305|PubMed:2269306}.
CC -!- SUBUNIT: MCR is a hexamer of two alpha, two beta, and two gamma chains,
CC forming a dimer of heterotrimers. {ECO:0000269|PubMed:2269306}.
CC -!- DEVELOPMENTAL STAGE: There are two MCR complexes in this bacteria. MCR
CC II is expressed in the early growth phase. Late growth cells contain
CC mostly MCR I. {ECO:0000269|PubMed:2269306,
CC ECO:0000269|PubMed:27467699}.
CC -!- PTM: The alpha subunit contains six modified amino acids near the
CC active site region. Is methylated on His-260, Arg-274, Gln-402 and Cys-
CC 454, probably by the action of specific S-adenosylmethionine-dependent
CC methyltransferases. Also contains a thioglycine at position 447,
CC forming a thiopeptide bond. Contains a didehydroaspartate residue at
CC position 452 (PubMed:27467699). The methylation on C5 of Arg-274 is a
CC post-translational methylation not essential in vivo, but which plays a
CC role for the stability and structural integrity of MCR (By similarity).
CC {ECO:0000250|UniProtKB:Q8THH1, 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; CP001710; ADL59091.1; -; Genomic_DNA.
DR RefSeq; WP_013296302.1; NC_014408.1.
DR PDB; 5A8R; X-ray; 2.15 A; A/D/G/J=1-553.
DR PDBsum; 5A8R; -.
DR AlphaFoldDB; P58815; -.
DR SMR; P58815; -.
DR STRING; 79929.MTBMA_c15120; -.
DR iPTMnet; P58815; -.
DR EnsemblBacteria; ADL59091; ADL59091; MTBMA_c15120.
DR GeneID; 9705221; -.
DR KEGG; mmg:MTBMA_c15120; -.
DR PATRIC; fig|79929.8.peg.1465; -.
DR HOGENOM; CLU_493170_0_0_2; -.
DR OMA; VGHQPEY; -.
DR OrthoDB; 6589at2157; -.
DR UniPathway; UPA00646; UER00699.
DR Proteomes; UP000000345; Chromosome.
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; Direct protein sequencing; Metal-binding; Methanogenesis;
KW Methylation; Nickel; Transferase.
FT CHAIN 1..553
FT /note="Methyl-coenzyme M reductase II subunit alpha"
FT /id="PRO_0000147458"
FT BINDING 150
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:27467699,
FT ECO:0007744|PDB:5A8R"
FT BINDING 228
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:27467699,
FT ECO:0007744|PDB:5A8R"
FT BINDING 259..260
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:27467699,
FT ECO:0007744|PDB:5A8R"
FT BINDING 273
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:27467699,
FT ECO:0007744|PDB:5A8R"
FT BINDING 335
FT /ligand="coenzyme M"
FT /ligand_id="ChEBI:CHEBI:58319"
FT /evidence="ECO:0000269|PubMed:27467699,
FT ECO:0007744|PDB:5A8R"
FT BINDING 446
FT /ligand="coenzyme M"
FT /ligand_id="ChEBI:CHEBI:58319"
FT /evidence="ECO:0000269|PubMed:27467699,
FT ECO:0007744|PDB:5A8R"
FT MOD_RES 260
FT /note="Pros-methylhistidine"
FT /evidence="ECO:0000269|PubMed:27467699"
FT MOD_RES 274
FT /note="5-methylarginine"
FT /evidence="ECO:0000269|PubMed:27467699"
FT MOD_RES 402
FT /note="2-methylglutamine"
FT /evidence="ECO:0000269|PubMed:27467699"
FT MOD_RES 447
FT /note="1-thioglycine"
FT /evidence="ECO:0000269|PubMed:27467699"
FT MOD_RES 452
FT /note="(Z)-2,3-didehydroaspartate"
FT /evidence="ECO:0000269|PubMed:27467699"
FT MOD_RES 454
FT /note="S-methylcysteine"
FT /evidence="ECO:0000269|PubMed:27467699"
FT CONFLICT 2
FT /note="D -> L (in Ref. 2; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 8..14
FT /evidence="ECO:0007829|PDB:5A8R"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 32..35
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 37..48
FT /evidence="ECO:0007829|PDB:5A8R"
FT TURN 49..55
FT /evidence="ECO:0007829|PDB:5A8R"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:5A8R"
FT STRAND 74..77
FT /evidence="ECO:0007829|PDB:5A8R"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 86..89
FT /evidence="ECO:0007829|PDB:5A8R"
FT TURN 91..93
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 95..105
FT /evidence="ECO:0007829|PDB:5A8R"
FT STRAND 107..112
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 113..121
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 129..142
FT /evidence="ECO:0007829|PDB:5A8R"
FT TURN 143..145
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 158..160
FT /evidence="ECO:0007829|PDB:5A8R"
FT STRAND 165..171
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 173..178
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 181..183
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 187..190
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 193..203
FT /evidence="ECO:0007829|PDB:5A8R"
FT STRAND 207..212
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 215..220
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 225..241
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 251..259
FT /evidence="ECO:0007829|PDB:5A8R"
FT TURN 260..262
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 272..274
FT /evidence="ECO:0007829|PDB:5A8R"
FT STRAND 278..280
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 281..283
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 286..292
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 295..297
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 302..317
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 318..325
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 333..337
FT /evidence="ECO:0007829|PDB:5A8R"
FT TURN 338..340
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 344..359
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 369..389
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 391..396
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 400..419
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 422..440
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 455..459
FT /evidence="ECO:0007829|PDB:5A8R"
FT TURN 464..466
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 470..472
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 478..480
FT /evidence="ECO:0007829|PDB:5A8R"
FT STRAND 484..486
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 487..501
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 509..514
FT /evidence="ECO:0007829|PDB:5A8R"
FT STRAND 520..522
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 527..535
FT /evidence="ECO:0007829|PDB:5A8R"
FT HELIX 546..548
FT /evidence="ECO:0007829|PDB:5A8R"
SQ SEQUENCE 553 AA; 60678 MW; 94CC0D641E7C8271 CRC64;
MDEKKLFLKA LKKKFEGEDP DEKYTNFYCF GGWEQSARKK EFTEYAKKAA EKRGGIPFYN
PDIGVPLGQR KLMAYRVSGT DAYVEGDDLH FVNNAAIQQM VDDIKRTVIV GMDTAHAVLE
KRLGVEVTPE TINEYMEAIN HALPGGAVVQ EHMVEVHPGL VEDCYAKIFT GDDNLADELD
KRILIDINKE FPEEQAEQLK SYIGNRTYQV NRVPTIVVRT CDGGTVSRWS AMQIGMSFIS
AYKLCAGEAA IADFSYAAKH ADVIEMGTIM PARRARGPNE PGGVAFGTFA DIVQTSRVSD
DPANVSLEVI AGAAALYDQV WLGSYMSGGV GFTQYATAAY TDDILDDFVY YGMEYVDDKY
GICGTKPTMD VVRDISTEVT LYSLEQYEEY PTLLEDHFGG SQRAAVAAAA AGCSTAFATG
NSNAGINGWY LSQILHKEAH SRLGFYGYDL QDQCGASNSL SIRSDEGLIH ELRGPNYPNY
AMNVGHQPEY AGIAQAPHAA RGDAFCTNPL IKVAFADKDL AFDFTSPRKS IAAGALREFM
PEGERDLIIP AGK
