RASEA_THEKO
ID RASEA_THEKO Reviewed; 324 AA.
AC Q5JE80;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 91.
DE RecName: Full=Archaeosine synthase subunit beta {ECO:0000303|PubMed:31740832};
DE EC=4.3.2.- {ECO:0000305|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=TK1135 {ECO:0000312|EMBL:BAD85324.1};
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, DISRUPTION PHENOTYPE, PATHWAY,
RP INTERACTION WITH ARCS, AND REACTION MECHANISM.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
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:0000305|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, likely an alpha(2)beta(2) heterotetrameric structure.
CC {ECO:0000269|PubMed:31740832}.
CC -!- DISRUPTION PHENOTYPE: Archaeosine is no more detected among the
CC modified nucleosides in tRNA fractions, but a nucleoside corresponding
CC to q0kN can be observed. {ECO:0000269|PubMed:31740832}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. RaSEA family.
CC {ECO:0000305}.
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DR EMBL; AP006878; BAD85324.1; -; Genomic_DNA.
DR RefSeq; WP_011250086.1; NC_006624.1.
DR AlphaFoldDB; Q5JE80; -.
DR SMR; Q5JE80; -.
DR STRING; 69014.TK1135; -.
DR EnsemblBacteria; BAD85324; BAD85324; TK1135.
DR GeneID; 3234076; -.
DR KEGG; tko:TK1135; -.
DR PATRIC; fig|69014.16.peg.1111; -.
DR eggNOG; arCOG01360; Archaea.
DR HOGENOM; CLU_060488_0_0_2; -.
DR InParanoid; Q5JE80; -.
DR OMA; KRGPHNC; -.
DR OrthoDB; 29724at2157; -.
DR PhylomeDB; Q5JE80; -.
DR BRENDA; 2.6.1.B20; 5246.
DR UniPathway; UPA00393; -.
DR Proteomes; UP000000536; 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 Pfam; PF04055; Radical_SAM; 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..324
FT /note="Archaeosine synthase subunit beta"
FT /id="PRO_0000450073"
FT DOMAIN 12..254
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 27
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:Q8THK1"
FT BINDING 36
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:Q8THK1"
FT BINDING 39
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:Q8THK1"
SQ SEQUENCE 324 AA; 36996 MW; 891C43BC3F76E501 CRC64;
MTYWTSEDNV AGKPGTALFI ILPTIGCYRY RIGQACYMCS YPTAAPKVKW TQEAIVNYVK
EALEKIEGTE GPFAVRMFTS GSFLDNGELK PETRRKIFEI LAEMDNVEEI VIESRSELVR
YEAVKELAEI VPDKHFEVAI GLETANDDVA DVSINKGNTF ADFVKAAEIT HKAGAKVKTY
LLLKPIFLSE RDGVEDAKES IIKAEPYTDT FSINITDIQK GTLYERLWEK KEYRPPWLWS
AVEVLIWAKR KFPNKRILSD PVGAGSKRGP HNCLTDYDRV IGKAIKKFSA TQDLSYIENL
KPECRDRWEY IVENGLLDWQ LVTW
