RTCB_METMP
ID RTCB_METMP Reviewed; 480 AA.
AC Q6LXF9;
DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 79.
DE RecName: Full=tRNA-splicing ligase RtcB {ECO:0000250|UniProtKB:O59245};
DE EC=6.5.1.8 {ECO:0000250|UniProtKB:O59245};
DE AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000250|UniProtKB:O59245};
GN Name=rtcB; OrderedLocusNames=MMP1392;
OS Methanococcus maripaludis (strain S2 / LL).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanococcaceae; Methanococcus.
OX NCBI_TaxID=267377;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=S2 / LL;
RX PubMed=15466049; DOI=10.1128/jb.186.20.6956-6969.2004;
RA Hendrickson E.L., Kaul R., Zhou Y., Bovee D., Chapman P., Chung J.,
RA Conway de Macario E., Dodsworth J.A., Gillett W., Graham D.E., Hackett M.,
RA Haydock A.K., Kang A., Land M.L., Levy R., Lie T.J., Major T.A.,
RA Moore B.C., Porat I., Palmeiri A., Rouse G., Saenphimmachak C., Soell D.,
RA Van Dien S., Wang T., Whitman W.B., Xia Q., Zhang Y., Larimer F.W.,
RA Olson M.V., Leigh J.A.;
RT "Complete genome sequence of the genetically tractable hydrogenotrophic
RT methanogen Methanococcus maripaludis.";
RL J. Bacteriol. 186:6956-6969(2004).
CC -!- FUNCTION: Essential for tRNA splicing and maturation. Acts by directly
CC joining spliced tRNA halves to mature-sized tRNAs. Joins RNA with
CC 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy
CC ends. {ECO:0000250|UniProtKB:O59245}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'-end 3'-phospho-ribonucleotide-RNA + a 5'-end dephospho-
CC ribonucleoside-RNA + GTP = a ribonucleotidyl-ribonucleotide-RNA +
CC diphosphate + GMP; Xref=Rhea:RHEA:68076, Rhea:RHEA-COMP:10463,
CC Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:17355, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:37565, ChEBI:CHEBI:58115, ChEBI:CHEBI:83062,
CC ChEBI:CHEBI:138284, ChEBI:CHEBI:173118; EC=6.5.1.8;
CC Evidence={ECO:0000250|UniProtKB:O59245};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + a 5'-end
CC dephospho-ribonucleoside-RNA + GTP + H2O = a ribonucleotidyl-
CC ribonucleotide-RNA + diphosphate + GMP + H(+); Xref=Rhea:RHEA:68080,
CC Rhea:RHEA-COMP:10464, Rhea:RHEA-COMP:13936, Rhea:RHEA-COMP:17355,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:37565, ChEBI:CHEBI:58115, ChEBI:CHEBI:83064,
CC ChEBI:CHEBI:138284, ChEBI:CHEBI:173118; EC=6.5.1.8;
CC Evidence={ECO:0000250|UniProtKB:O59245};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:O59245};
CC Note=Binds 2 manganese ions per subunit.
CC {ECO:0000250|UniProtKB:O59245};
CC -!- SUBUNIT: Monomer. {ECO:0000250|UniProtKB:O59245}.
CC -!- MISCELLANEOUS: Ligation proceeds through 3 nucleotidyl transfer steps,
CC with 2',3'-cyclic phosphate termini being hydrolyzed to 3'-P termini in
CC a step that precedes 3'-P activation with GMP. In the first nucleotidyl
CC transfer step, RtcB reacts with GTP to form a covalent RtcB-histidine-
CC GMP intermediate with release of PPi; in the second step, the GMP
CC moiety is transferred to the RNA 3'-P; in the third step, the 5'-OH
CC from the opposite RNA strand attacks the activated 3'-P to form a
CC 3',5'-phosphodiester bond and release GMP.
CC {ECO:0000250|UniProtKB:O59245}.
CC -!- SIMILARITY: Belongs to the RtcB family. {ECO:0000305}.
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DR EMBL; BX950229; CAF30948.1; -; Genomic_DNA.
DR RefSeq; WP_011171336.1; NC_005791.1.
DR AlphaFoldDB; Q6LXF9; -.
DR SMR; Q6LXF9; -.
DR STRING; 267377.MMP1392; -.
DR PRIDE; Q6LXF9; -.
DR EnsemblBacteria; CAF30948; CAF30948; MMP1392.
DR GeneID; 2762660; -.
DR KEGG; mmp:MMP1392; -.
DR PATRIC; fig|267377.15.peg.1428; -.
DR eggNOG; arCOG04246; Archaea.
DR HOGENOM; CLU_022279_0_1_2; -.
DR OMA; QTRGVEC; -.
DR OrthoDB; 22545at2157; -.
DR BioCyc; MMAR267377:MMP_RS07165-MON; -.
DR Proteomes; UP000000590; Chromosome.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008452; F:RNA ligase activity; IEA:InterPro.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 3.90.1860.10; -; 1.
DR InterPro; IPR001233; RtcB.
DR InterPro; IPR036025; RtcB-like_sf.
DR PANTHER; PTHR11118; PTHR11118; 1.
DR Pfam; PF01139; RtcB; 1.
DR SUPFAM; SSF103365; SSF103365; 1.
DR PROSITE; PS01288; UPF0027; 1.
PE 3: Inferred from homology;
KW GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome; tRNA processing.
FT CHAIN 1..480
FT /note="tRNA-splicing ligase RtcB"
FT /id="PRO_0000232541"
FT ACT_SITE 403
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 95
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 98
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 98
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 202..206
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 203
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 234
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 328..329
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 328
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 377..380
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 384
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 403..406
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 479
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
SQ SEQUENCE 480 AA; 52801 MW; 5FC5B6C9D9C67910 CRC64;
MKSTVTKIAE KTYQLPVSYK DCMRVPGNVY LDELLFENLQ EDVFEQIANV ACLPGIQKYS
LAMPDCHYGY GFCIGGVAAF DEVTGVISPG GVGFDINCGV RLVKTNLTKN DVTPKLKELL
SEIFKNVPSG LGSKGKIRIT KDEIDSVLEE GVSWAVEEEY GWERDIKHIE EHGKMKEADP
TLVSDNAKKR GLPQLGSLGS GNHFLEVQYV DEIFDEEAAK TFGVSPDQVV LMIHTGSRGL
GHQICADYLR YMENAAKKYN IKLPDRQLAC APINSEEGQK YFKAMSCGAN YAWANRQLIT
HWIRESFESV FKTSAEDLEM DIIYDVAHNI AKKEQHLVDG VLKNVVVHRK GATRAFGPGH
AEIPSDYVNI GQPVIIPGDM GTASYLMHGT EKAMEQTFGS TAHGAGRALS RVKALKLYTG
NEVQEALQKK GILVMADSKG VIAEECPEAY KDIENVADIC HDSGISLKVA KMKPMGVVKG
