RTCB_NANEQ
ID RTCB_NANEQ Reviewed; 477 AA.
AC Q74MJ0;
DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 74.
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=NEQ078;
OS Nanoarchaeum equitans (strain Kin4-M).
OC Archaea; Nanoarchaeota; Candidatus Nanoarchaeia; Nanoarchaeales;
OC Nanoarchaeaceae; Nanoarchaeum.
OX NCBI_TaxID=228908;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Kin4-M;
RX PubMed=14566062; DOI=10.1073/pnas.1735403100;
RA Waters E., Hohn M.J., Ahel I., Graham D.E., Adams M.D., Barnstead M.,
RA Beeson K.Y., Bibbs L., Bolanos R., Keller M., Kretz K., Lin X., Mathur E.,
RA Ni J., Podar M., Richardson T., Sutton G.G., Simon M., Soell D.,
RA Stetter K.O., Short J.M., Noorderwier M.;
RT "The genome of Nanoarchaeum equitans: insights into early archaeal
RT evolution and derived parasitism.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:12984-12988(2003).
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; AE017199; AAR38934.1; -; Genomic_DNA.
DR AlphaFoldDB; Q74MJ0; -.
DR SMR; Q74MJ0; -.
DR STRING; 228908.NEQ078; -.
DR EnsemblBacteria; AAR38934; AAR38934; NEQ078.
DR KEGG; neq:NEQ078; -.
DR PATRIC; fig|228908.8.peg.81; -.
DR HOGENOM; CLU_022279_0_1_2; -.
DR OMA; QTRGVEC; -.
DR Proteomes; UP000000578; 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.
PE 3: Inferred from homology;
KW GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome; tRNA processing.
FT CHAIN 1..477
FT /note="tRNA-splicing ligase RtcB"
FT /id="PRO_0000232542"
FT ACT_SITE 400
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 94
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 97
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 97
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 201..205
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 202
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 325..326
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 325
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 374..377
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 381
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 400..403
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 476
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
SQ SEQUENCE 477 AA; 53730 MW; 9C56F4D217096B0B CRC64;
MDIKLRKIDK YIWEIPKEGK MNVPVRIYAS DKLIEKMKED RTLIQARNVS MLPKIVKHMV
VMPDGHEGYG PPIGGVGAFS LDNPPVIPGF VGFDINCGVR LLRTNLTIDE IKDRLNLLVN
EIFRNVPAGV GEGGKLKLSI DELNKVLDYG VNWAIDNGFG WEEDRNRIES HGYLDFADSD
AVSNTAKQRG KDQLGTIGSG NHFLEIQVVD QIYDEEIAKA FGIYEKNQVT VLIHTGSRGL
GHQVASDYLR LFEKKYKYDV PDRELIYAPY DSKDAQNYLK AMAAAANFAW ANRQLITYWV
RKSFEKVLRK NIESIGLEIV YDLAHNIAKF EEHTIDGKKQ KLIVYRKGAT RAFPPGHKEL
WGEYKKYGQP VIIPGSMGTA SYLLVGQPKA MELSFGSSAH GAGRQLSRVK AKKLYSYSEV
IRKLREMGII VKSTTKTGVL EEIPEAYKDI DEVVRVTHEL GISKIVARFR PVAVIKG
