RASEA_METAC
ID RASEA_METAC Reviewed; 346 AA.
AC Q8THK1;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 17-JUN-2020, sequence version 2.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=Archaeosine synthase subunit beta {ECO:0000303|PubMed:31740832};
DE EC=4.3.2.- {ECO:0000269|PubMed:31740832};
DE AltName: Full=Archaeosine synthase, q0kN-tRNA lyase subunit {ECO:0000303|PubMed:31740832};
DE AltName: Full=Radical SAM enzyme for archaeosine formation {ECO:0000303|PubMed:31740832};
DE Short=RaSEA {ECO:0000303|PubMed:31740832};
GN OrderedLocusNames=MA_4513 {ECO:0000312|EMBL:AAM07853.1};
OS Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 /
OS C2A).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=188937;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35395 / DSM 2834 / JCM 12185 / C2A;
RX PubMed=11932238; DOI=10.1101/gr.223902;
RA Galagan J.E., Nusbaum C., Roy A., Endrizzi M.G., Macdonald P., FitzHugh W.,
RA Calvo S., Engels R., Smirnov S., Atnoor D., Brown A., Allen N., Naylor J.,
RA Stange-Thomann N., DeArellano K., Johnson R., Linton L., McEwan P.,
RA McKernan K., Talamas J., Tirrell A., Ye W., Zimmer A., Barber R.D.,
RA Cann I., Graham D.E., Grahame D.A., Guss A.M., Hedderich R.,
RA Ingram-Smith C., Kuettner H.C., Krzycki J.A., Leigh J.A., Li W., Liu J.,
RA Mukhopadhyay B., Reeve J.N., Smith K., Springer T.A., Umayam L.A.,
RA White O., White R.H., de Macario E.C., Ferry J.G., Jarrell K.F., Jing H.,
RA Macario A.J.L., Paulsen I.T., Pritchett M., Sowers K.R., Swanson R.V.,
RA Zinder S.H., Lander E., Metcalf W.W., Birren B.;
RT "The genome of Methanosarcina acetivorans reveals extensive metabolic and
RT physiological diversity.";
RL Genome Res. 12:532-542(2002).
RN [2]
RP FUNCTION, COFACTOR, CATALYTIC ACTIVITY, PATHWAY, INTERACTION WITH ARCS,
RP MUTAGENESIS OF CYS-51; CYS-59 AND CYS-62, AND REACTION MECHANISM.
RX PubMed=31740832; DOI=10.1038/s41589-019-0390-7;
RA Yokogawa T., Nomura Y., Yasuda A., Ogino H., Hiura K., Nakada S., Oka N.,
RA Ando K., Kawamura T., Hirata A., Hori H., Ohno S.;
RT "Identification of a radical SAM enzyme involved in the synthesis of
RT archaeosine.";
RL Nat. Chem. Biol. 15:1148-1155(2019).
CC -!- FUNCTION: Radical SAM enzyme involved in the synthesis of archaeosine,
CC a modified nucleoside present in the dihydrouridine loop (D-loop) of
CC archaeal tRNAs. Catalyzes the cleavage of the C(epsilon)-N bond of the
CC lysine moiety of q0kN15-tRNA, leading to the formation of archaeosine
CC at position 15 in tRNAs. {ECO:0000269|PubMed:31740832}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=7-N-[(5S)-5-amino-5-carboxypentyl]formamidino-7-
CC deazaguanosine(15) in tRNA + S-adenosyl-L-methionine = 5'-
CC deoxyadenosine + archaeosine(15) in tRNA + 2 H(+) + L-1-piperideine-
CC 6-carboxylate + L-methionine; Xref=Rhea:RHEA:63220, Rhea:RHEA-
CC COMP:14170, Rhea:RHEA-COMP:16288, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17319, ChEBI:CHEBI:57844, ChEBI:CHEBI:58769,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:138803, ChEBI:CHEBI:145542;
CC Evidence={ECO:0000269|PubMed:31740832};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:63221;
CC Evidence={ECO:0000269|PubMed:31740832};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:31740832};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000305|PubMed:31740832};
CC -!- PATHWAY: tRNA modification; archaeosine-tRNA biosynthesis.
CC {ECO:0000269|PubMed:31740832}.
CC -!- SUBUNIT: Forms a robust complex with the archaeosine synthase alpha
CC subunit ArcS (PubMed:31740832). This complex likely consists of an
CC alpha(2)beta(2) heterotetrameric structure (By similarity).
CC {ECO:0000250|UniProtKB:Q5JE80, ECO:0000269|PubMed:31740832}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. RaSEA family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM07853.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AE010299; AAM07853.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_048066004.1; NC_003552.1.
DR AlphaFoldDB; Q8THK1; -.
DR SMR; Q8THK1; -.
DR STRING; 188937.MA_4513; -.
DR EnsemblBacteria; AAM07853; AAM07853; MA_4513.
DR GeneID; 1476407; -.
DR KEGG; mac:MA_4513; -.
DR HOGENOM; CLU_060488_0_0_2; -.
DR InParanoid; Q8THK1; -.
DR PhylomeDB; Q8THK1; -.
DR BRENDA; 2.6.1.B20; 7224.
DR UniPathway; UPA00393; -.
DR Proteomes; UP000002487; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0002926; P:tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation; IBA:GO_Central.
DR InterPro; IPR039661; ELP3.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR005909; RaSEA.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR11135; PTHR11135; 1.
DR PIRSF; PIRSF004954; Radical_SAM; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR01210; TIGR01210; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Iron; Iron-sulfur; Lyase; Metal-binding; Reference proteome;
KW S-adenosyl-L-methionine; tRNA processing.
FT CHAIN 1..346
FT /note="Archaeosine synthase subunit beta"
FT /id="PRO_0000450072"
FT DOMAIN 36..276
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 51
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000269|PubMed:31740832"
FT BINDING 59
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000269|PubMed:31740832"
FT BINDING 62
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000269|PubMed:31740832"
FT MUTAGEN 51
FT /note="C->A: Loss of archaeosine formation."
FT /evidence="ECO:0000269|PubMed:31740832"
FT MUTAGEN 59
FT /note="C->A: Loss of archaeosine formation."
FT /evidence="ECO:0000269|PubMed:31740832"
FT MUTAGEN 62
FT /note="C->A: Loss of archaeosine formation."
FT /evidence="ECO:0000269|PubMed:31740832"
SQ SEQUENCE 346 AA; 38704 MW; 96C046C86EE4BECB CRC64;
MSLNKAVLEI RQRIKVKPSP TNEPAASWTG TDLVNGVQTK TLTVIFKSAG CRWGKAGGCT
MCGYVYDCAS EPPSLEDYMA QLEKAMRKAE KFPEFMVKIF TSGSFLDEQE VLPEARDAIL
KNLTEDPRVT KVLVETRPNY VTEENVQACL SILKNKPFEL AFGLETSSDK IRRDSINKGF
TFQDFVHAAE TAKKYGVTVK VYLMLKPLFL SERQAMEDII RSIDDAAPYA DTISINLCNV
QKGTLVEALW EKGQYRPPWL WSIIEILRQA KAAHPELPLM SDPVGAGSKR GPHNCKICSS
EVADSLRTFS LTQNPADLST ADCECKELWK KVLEIEDFTY GTPILD
