RTCB_ECOLI
ID RTCB_ECOLI Reviewed; 408 AA.
AC P46850; P76690; Q2M785;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 3.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=RNA-splicing ligase RtcB {ECO:0000305};
DE EC=6.5.1.8 {ECO:0000269|PubMed:22474365, ECO:0000269|PubMed:24218597, ECO:0000269|PubMed:26858100};
DE AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000305};
GN Name=rtcB {ECO:0000303|PubMed:9738023}; Synonyms=yhgL;
GN OrderedLocusNames=b3421, JW3384;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP GENE NAME, AND INDUCTION.
RX PubMed=9738023; DOI=10.1074/jbc.273.39.25516;
RA Genschik P., Drabikowski K., Filipowicz W.;
RT "Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase
RT and its sigma54-regulated operon.";
RL J. Biol. Chem. 273:25516-25526(1998).
RN [4]
RP FUNCTION, SUBUNIT, AND INDUCTION.
RC STRAIN=K12;
RX PubMed=21224389; DOI=10.1074/jbc.c111.219022;
RA Tanaka N., Shuman S.;
RT "RtcB is the RNA ligase component of an Escherichia coli RNA repair
RT operon.";
RL J. Biol. Chem. 286:7727-7731(2011).
RN [5]
RP FUNCTION, AND COFACTOR.
RX PubMed=21757685; DOI=10.1074/jbc.c111.274597;
RA Tanaka N., Meineke B., Shuman S.;
RT "RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA
RT splicing in vivo.";
RL J. Biol. Chem. 286:30253-30257(2011).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
RX PubMed=22045815; DOI=10.1074/jbc.m111.302133;
RA Tanaka N., Chakravarty A.K., Maughan B., Shuman S.;
RT "Novel mechanism of RNA repair by RtcB via sequential 2',3'-cyclic
RT phosphodiesterase and 3'-Phosphate/5'-hydroxyl ligation reactions.";
RL J. Biol. Chem. 286:43134-43143(2011).
RN [7]
RP FUNCTION.
RX PubMed=22730297; DOI=10.1093/nar/gks558;
RA Chakravarty A.K., Shuman S.;
RT "The sequential 2',3'-cyclic phosphodiesterase and 3'-phosphate/5'-OH
RT ligation steps of the RtcB RNA splicing pathway are GTP-dependent.";
RL Nucleic Acids Res. 40:8558-8567(2012).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION BY MASS SPECTROMETRY, ACTIVE
RP SITE, REACTION MECHANISM, AND MUTAGENESIS OF HIS-337.
RX PubMed=22474365; DOI=10.1073/pnas.1201207109;
RA Chakravarty A.K., Subbotin R., Chait B.T., Shuman S.;
RT "RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-
RT (histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:6072-6077(2012).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, AND REACTION MECHANISM.
RX PubMed=24218597; DOI=10.1073/pnas.1314289110;
RA Das U., Chakravarty A.K., Remus B.S., Shuman S.;
RT "Rewriting the rules for end joining via enzymatic splicing of DNA 3'-PO4
RT and 5'-OH ends.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:20437-20442(2013).
RN [10]
RP FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, AND MUTAGENESIS OF
RP ASP-75; CYS-78; ASN-167; HIS-168; HIS-185; ARG-189; HIS-281; LYS-299;
RP HIS-337; ARG-341 AND ARG-345.
RX PubMed=26858100; DOI=10.1128/jb.00913-15;
RA Maughan W.P., Shuman S.;
RT "Distinct contributions of enzymic functional groups to the 2',3'-cyclic
RT phosphodiesterase, 3'-phosphate guanylylation, and 3'-ppG/5'-OH ligation
RT steps of the Escherichia coli RtcB nucleic acid splicing pathway.";
RL J. Bacteriol. 198:1294-1304(2016).
CC -!- FUNCTION: GTP-dependent RNA ligase that is involved in tRNA splicing
CC and RNA repair (PubMed:21224389, PubMed:21757685, PubMed:22045815,
CC PubMed:22730297, PubMed:22474365, PubMed:26858100). Joins RNA with
CC 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy ends
CC (PubMed:21224389, PubMed:21757685, PubMed:22045815, PubMed:22730297,
CC PubMed:22474365, PubMed:26858100). Also acts as a DNA ligase in case of
CC DNA damage by splicing 'dirty' DNA breaks, characterized by 3'-
CC phosphate (or cyclic-phosphate) and 5'-hydroxy ends that cannot be
CC sealed by classical DNA ligases (PubMed:24218597).
CC {ECO:0000269|PubMed:21224389, ECO:0000269|PubMed:21757685,
CC ECO:0000269|PubMed:22045815, ECO:0000269|PubMed:22474365,
CC ECO:0000269|PubMed:22730297, ECO:0000269|PubMed:24218597,
CC ECO:0000269|PubMed:26858100}.
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:0000269|PubMed:22045815, ECO:0000269|PubMed:22474365,
CC ECO:0000269|PubMed:24218597, ECO:0000269|PubMed:26858100};
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:0000269|PubMed:22045815, ECO:0000269|PubMed:22474365,
CC ECO:0000269|PubMed:24218597, ECO:0000269|PubMed:26858100};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:21757685, ECO:0000269|PubMed:22045815};
CC Note=Binds 2 manganese ions per subunit.
CC {ECO:0000250|UniProtKB:O59245};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:21224389}.
CC -!- INDUCTION: Expression is repressed by RtcR.
CC {ECO:0000269|PubMed:21224389, ECO:0000269|PubMed:9738023}.
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 (PubMed:22474365,
CC PubMed=26858100). Acts as a DNA ligase by attaching a GMP nucleotide to
CC a DNA 3'-P to form a 'capped' 3' end structure, DNA3'pp5'G. When a
CC suitable DNA 5'-OH end is available, RtcB catalyzes attack of the 5'-OH
CC on DNA3'pp5'G to form a 3'-5' phosphodiester splice junction
CC (PubMed:24218597). {ECO:0000305|PubMed:22474365,
CC ECO:0000305|PubMed:24218597, ECO:0000305|PubMed:26858100}.
CC -!- SIMILARITY: Belongs to the RtcB family. {ECO:0000305}.
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DR EMBL; U18997; AAA58219.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76446.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77871.1; -; Genomic_DNA.
DR PIR; H65137; H65137.
DR RefSeq; NP_417879.1; NC_000913.3.
DR RefSeq; WP_001105504.1; NZ_SSZK01000008.1.
DR AlphaFoldDB; P46850; -.
DR SMR; P46850; -.
DR BioGRID; 4261188; 7.
DR IntAct; P46850; 20.
DR STRING; 511145.b3421; -.
DR SWISS-2DPAGE; P46850; -.
DR PaxDb; P46850; -.
DR PRIDE; P46850; -.
DR EnsemblBacteria; AAC76446; AAC76446; b3421.
DR EnsemblBacteria; BAE77871; BAE77871; BAE77871.
DR GeneID; 947929; -.
DR KEGG; ecj:JW3384; -.
DR KEGG; eco:b3421; -.
DR PATRIC; fig|511145.12.peg.3516; -.
DR EchoBASE; EB2774; -.
DR eggNOG; COG1690; Bacteria.
DR HOGENOM; CLU_022279_1_1_6; -.
DR InParanoid; P46850; -.
DR OMA; QTRGVEC; -.
DR PhylomeDB; P46850; -.
DR BioCyc; EcoCyc:G7751-MON; -.
DR BioCyc; MetaCyc:G7751-MON; -.
DR BRENDA; 6.5.1.4; 2026.
DR BRENDA; 6.5.1.8; 2026.
DR PRO; PR:P46850; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0003909; F:DNA ligase activity; IDA:EcoCyc.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0008452; F:RNA ligase activity; IDA:EcoCyc.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IDA:UniProtKB.
DR GO; GO:0006281; P:DNA repair; IDA:UniProtKB.
DR GO; GO:0006396; P:RNA processing; IDA:UniProtKB.
DR GO; GO:0042245; P:RNA repair; EXP:EcoCyc.
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 Pfam; PF01139; RtcB; 1.
DR SUPFAM; SSF103365; SSF103365; 1.
DR PROSITE; PS01288; UPF0027; 1.
PE 1: Evidence at protein level;
KW GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome; tRNA processing.
FT CHAIN 1..408
FT /note="RNA-splicing ligase RtcB"
FT /id="PRO_0000215109"
FT ACT_SITE 337
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000269|PubMed:22474365"
FT BINDING 75
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 78
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 78
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 167..171
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 168
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 185
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 281..282
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 281
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 313..316
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 320
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 337..340
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 407
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT MUTAGEN 75
FT /note="D->A: Almost no guanylation activity. Can ligate
FT pre-guanylated nucleotide substrates."
FT /evidence="ECO:0000269|PubMed:26858100"
FT MUTAGEN 78
FT /note="C->A: No activity."
FT /evidence="ECO:0000269|PubMed:26858100"
FT MUTAGEN 167
FT /note="N->A: Retains approximately half of overall wild-
FT type activity. Shows increased nucleotide guanylation
FT activity."
FT /evidence="ECO:0000269|PubMed:26858100"
FT MUTAGEN 168
FT /note="H->A: Retains approximately half of overall wild-
FT type activity."
FT /evidence="ECO:0000269|PubMed:26858100"
FT MUTAGEN 185
FT /note="H->A: Almost wild type activity. Is impaired in DNA
FT 3'-phosphate capping."
FT /evidence="ECO:0000269|PubMed:26858100"
FT MUTAGEN 189
FT /note="R->A: Almost wild type activity. Shows increased
FT nucleotide guanylation activity."
FT /evidence="ECO:0000269|PubMed:26858100"
FT MUTAGEN 281
FT /note="H->A: Less than 10% of overall wild-type activity.
FT Can ligate pre-guanylated nucleotide substrates."
FT /evidence="ECO:0000269|PubMed:26858100"
FT MUTAGEN 299
FT /note="K->A: Retains approximately half of overall wild-
FT type activity."
FT /evidence="ECO:0000269|PubMed:26858100"
FT MUTAGEN 337
FT /note="H->A: No overall activity. Abolishes formation of
FT guanylylated RtcB intermediate. Can ligate pre-guanylated
FT nucleotide substrates."
FT /evidence="ECO:0000269|PubMed:22474365,
FT ECO:0000269|PubMed:26858100"
FT MUTAGEN 337
FT /note="H->N,Q: Loss of function. Abolishes formation of
FT guanylylated RtcB intermediate."
FT /evidence="ECO:0000269|PubMed:22474365"
FT MUTAGEN 341
FT /note="R->A: Less than 10% of overall wild-type activity.
FT Shows increased nucleotide guanylation activity."
FT /evidence="ECO:0000269|PubMed:26858100"
FT MUTAGEN 345
FT /note="R->A: Almost wild type activity. Is impaired in DNA
FT 3'-phosphate capping."
FT /evidence="ECO:0000269|PubMed:26858100"
FT CONFLICT 84
FT /note="R -> G (in Ref. 1; AAA58219)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 408 AA; 45222 MW; C0C33BA04542185F CRC64;
MNYELLTTEN APVKMWTKGV PVEADARQQL INTAKMPFIF KHIAVMPDVH LGKGSTIGSV
IPTKGAIIPA AVGVDIGCGM NALRTALTAE DLPENLAELR QAIETAVPHG RTTGRCKRDK
GAWENPPVNV DAKWAELEAG YQWLTQKYPR FLNTNNYKHL GTLGTGNHFI EICLDESDQV
WIMLHSGSRG IGNAIGTYFI DLAQKEMQET LETLPSRDLA YFMEGTEYFD DYLKAVAWAQ
LFASLNRDAM MENVVTALQS ITQKTVRQPQ TLAMEEINCH HNYVQKEQHF GEEIYVTRKG
AVSARAGQYG IIPGSMGAKS FIVRGLGNEE SFCSCSHGAG RVMSRTKAKK LFSVEDQIRA
TAHVECRKDA EVIDEIPMAY KDIDAVMAAQ SDLVEVIYTL RQVVCVKG
