RTCB_PYRAE
ID RTCB_PYRAE Reviewed; 484 AA.
AC Q8ZY09;
DT 18-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 85.
DE RecName: Full=tRNA-splicing ligase RtcB {ECO:0000305};
DE EC=6.5.1.8 {ECO:0000269|PubMed:21209330};
DE AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000250|UniProtKB:O59245};
DE AltName: Full=Archaeal 3'-phosphate RNA splicing ligase {ECO:0000303|PubMed:21209330};
GN Name=rtcB; OrderedLocusNames=PAE0998;
OS Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP
OS 104966 / NBRC 100827 / IM2).
OC Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae;
OC Pyrobaculum.
OX NCBI_TaxID=178306;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2;
RX PubMed=11792869; DOI=10.1073/pnas.241636498;
RA Fitz-Gibbon S.T., Ladner H., Kim U.-J., Stetter K.O., Simon M.I.,
RA Miller J.H.;
RT "Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum
RT aerophilum.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:984-989(2002).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF CYS-100; HIS-205
RP AND HIS-237.
RC STRAIN=ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2;
RX PubMed=21209330; DOI=10.1073/pnas.1018307108;
RA Englert M., Sheppard K., Aslanian A., Yates J.R. III, Soll D.;
RT "Archaeal 3'-phosphate RNA splicing ligase characterization identifies the
RT missing component in tRNA maturation.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:1290-1295(2011).
CC -!- FUNCTION: Essential for tRNA splicing and maturation (PubMed:21209330).
CC Acts by directly joining spliced tRNA halves to mature-sized tRNAs
CC (PubMed:21209330). Joins RNA with 2',3'-cyclic-phosphate or 3'-
CC phosphate ends to RNA with 5'-hydroxy ends (By similarity).
CC {ECO:0000250|UniProtKB:O59245, ECO:0000269|PubMed:21209330}.
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:0000269|PubMed:21209330};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:O59245};
CC Note=Binds 2 manganese ions per subunit (By similarity). Can use zinc
CC ions (PubMed:21209330) (PubMed:21209330).
CC {ECO:0000250|UniProtKB:O59245, ECO:0000269|PubMed:21209330};
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; AE009441; AAL63187.1; -; Genomic_DNA.
DR AlphaFoldDB; Q8ZY09; -.
DR SMR; Q8ZY09; -.
DR STRING; 178306.PAE0998; -.
DR PRIDE; Q8ZY09; -.
DR EnsemblBacteria; AAL63187; AAL63187; PAE0998.
DR KEGG; pai:PAE0998; -.
DR PATRIC; fig|178306.9.peg.742; -.
DR eggNOG; arCOG04246; Archaea.
DR HOGENOM; CLU_022279_0_1_2; -.
DR InParanoid; Q8ZY09; -.
DR OMA; QTRGVEC; -.
DR BRENDA; 6.5.1.8; 5239.
DR Proteomes; UP000002439; 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:0003972; F:RNA ligase (ATP) activity; IBA:GO_Central.
DR GO; GO:0008452; F:RNA ligase activity; TAS:UniProtKB.
DR GO; GO:0000971; P:tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate; IBA:GO_Central.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IDA:UniProtKB.
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 1: Evidence at protein level;
KW GTP-binding; Ligase; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome; tRNA processing.
FT CHAIN 1..484
FT /note="tRNA-splicing ligase RtcB"
FT /id="PRO_0000232543"
FT ACT_SITE 407
FT /note="GMP-histidine intermediate"
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 100
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 100
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 204..208
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 205
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 237
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 330..331
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 330
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 381..384
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 388
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 407..410
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT BINDING 483
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000250|UniProtKB:O59245"
FT MUTAGEN 100
FT /note="C->A: Abolishes tRNA ligase activity; when
FT associated with A-205 and A-237."
FT /evidence="ECO:0000269|PubMed:21209330"
FT MUTAGEN 205
FT /note="H->A: Abolishes tRNA ligase activity; when
FT associated with A-100 and A-237."
FT /evidence="ECO:0000269|PubMed:21209330"
FT MUTAGEN 237
FT /note="H->A: Abolishes tRNA ligase activity; when
FT associated with A-100 and A-205."
FT /evidence="ECO:0000269|PubMed:21209330"
SQ SEQUENCE 484 AA; 53843 MW; 34ACE407885F4B91 CRC64;
MRNIPINKIN DYVWEIPPGV KPCQKVPVRI YADSVLLEKM KSDMTLEQGI NVGCLPGIYR
WSIVLPDAHQ GYGFPIGGVA AIDAEEGVIS PGGIGYDINC GVRVLRTNLT EEDVRPKLKE
LVDTIFRLVP PGVGGTGHLR LSPSEFERVL AEGVEWAVQK GYGWAEDMEY IEERGSWKLA
DPSKVSEKAK ARGRDQLGTL GSGNHFLEIQ VVDKIYDEKI AKLFGIEREG QVVVMIHTGS
RGFGHQVATD YLLIMERKMR QWGLNLPDRE LAAAPLKDKV AEDYIKAMAS AANFAWTNRH
IIMHWVREAF KKVFGSIEKV GLEVVYDVAH NIAKLEEHVV DEKGTVRKVW VHRKGATRAF
PPGRSEIPAK YREVGQPVLI PGSMGTASWI LVGTHDAMRL TFGTAPHGAG RVLSREAAIR
MYPPHKVQEE MAKRGIIVRS AETEVISEEA PWAYKDVDRV VEAAHQVGFA KKVVRQRPIG
VVKG
