ID S9XQI5_CAMFR Unreviewed; 894 AA.
AC S9XQI5;
DT 16-OCT-2013, integrated into UniProtKB/TrEMBL.
DT 16-OCT-2013, sequence version 1.
DT 22-FEB-2023, entry version 31.
DE RecName: Full=RNA-splicing ligase RtcB homolog {ECO:0000256|HAMAP-Rule:MF_03144};
DE EC=6.5.1.8 {ECO:0000256|HAMAP-Rule:MF_03144};
DE AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000256|HAMAP-Rule:MF_03144};
GN Name=RTCB {ECO:0000256|HAMAP-Rule:MF_03144};
GN ORFNames=CB1_001262003 {ECO:0000313|EMBL:EPY77446.1};
OS Camelus ferus (Wild bactrian camel) (Camelus bactrianus ferus).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Tylopoda; Camelidae; Camelus.
OX NCBI_TaxID=419612 {ECO:0000313|EMBL:EPY77446.1, ECO:0000313|Proteomes:UP000030684};
RN [1] {ECO:0000313|EMBL:EPY77446.1, ECO:0000313|Proteomes:UP000030684}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=bactrian camel {ECO:0000313|Proteomes:UP000030684};
RX PubMed=23149746;
RG Bactrian Camels Genome Sequencing and Analysis Consortium;
RA Jirimutu, Wang Z., Ding G., Chen G., Sun Y., Sun Z., Zhang H., Wang L.,
RA Hasi S., Zhang Y., Li J., Shi Y., Xu Z., He C., Yu S., Li S., Zhang W.,
RA Batmunkh M., Ts B., Narenbatu, Unierhu, Bat-Ireedui S., Gao H.,
RA Baysgalan B., Li Q., Jia Z., Turigenbayila, Subudenggerile, Narenmanduhu,
RA Wang Z., Wang J., Pan L., Chen Y., Ganerdene Y., Dabxilt, Erdemt, Altansha,
RA Altansukh, Liu T., Cao M., Aruuntsever, Bayart, Hosblig, He F., Zha-ti A.,
RA Zheng G., Qiu F., Sun Z., Zhao L., Zhao W., Liu B., Li C., Chen Y.,
RA Tang X., Guo C., Liu W., Ming L., Temuulen, Cui A., Li Y., Gao J., Li J.,
RA Wurentaodi, Niu S., Sun T., Zhai Z., Zhang M., Chen C., Baldan T.,
RA Bayaer T., Li Y., Meng H.;
RT "Genome sequences of wild and domestic bactrian camels.";
RL Nat. Commun. 3:1202-1202(2012).
CC -!- FUNCTION: Catalytic subunit of the tRNA-splicing ligase complex that
CC acts by directly joining spliced tRNA halves to mature-sized tRNAs by
CC incorporating the precursor-derived splice junction phosphate into the
CC mature tRNA as a canonical 3',5'-phosphodiester. May act as an RNA
CC ligase with broad substrate specificity, and may function toward other
CC RNAs. {ECO:0000256|HAMAP-Rule:MF_03144}.
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:0000256|ARBA:ARBA00029282, ECO:0000256|HAMAP-
CC Rule:MF_03144};
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:0000256|ARBA:ARBA00029311, ECO:0000256|HAMAP-
CC Rule:MF_03144};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_03144,
CC ECO:0000256|PIRSR:PIRSR601233-3};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_03144, ECO:0000256|PIRSR:PIRSR601233-3};
CC -!- SUBUNIT: Catalytic component of the tRNA-splicing ligase complex.
CC {ECO:0000256|HAMAP-Rule:MF_03144}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_03144}.
CC -!- MISCELLANEOUS: Ligation probably proceeds through 3 nucleotidyl
CC transfer steps, with 2',3'-cyclic phosphate termini being hydrolyzed to
CC 3'-P termini in a step that precedes 3'-P activation with GMP. In the
CC first nucleotidyl transfer step, RTCB reacts with GTP to form a
CC covalent RTCB-histidine-GMP intermediate with release of PPi; in the
CC second step, the GMP moiety is transferred to the RNA 3'-P; in the
CC third step, the 5'-OH from the opposite RNA strand attacks the
CC activated 3'-P to form a 3',5'-phosphodiester bond and release GMP.
CC {ECO:0000256|HAMAP-Rule:MF_03144}.
CC -!- SIMILARITY: Belongs to the RtcB family. {ECO:0000256|ARBA:ARBA00008071,
CC ECO:0000256|HAMAP-Rule:MF_03144}.
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DR EMBL; KB017471; EPY77446.1; -; Genomic_DNA.
DR AlphaFoldDB; S9XQI5; -.
DR Proteomes; UP000030684; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0072669; C:tRNA-splicing ligase complex; IEA:UniProtKB-UniRule.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0008289; F:lipid binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003972; F:RNA ligase (ATP) activity; IEA:InterPro.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IEA:UniProtKB-UniRule.
DR Gene3D; 3.90.1860.10; tRNA-splicing ligase RtcB; 1.
DR HAMAP; MF_03144; RtcB_euk; 1.
DR InterPro; IPR017943; Bactericidal_perm-incr_a/b_dom.
DR InterPro; IPR001124; Lipid-bd_serum_glycop_C.
DR InterPro; IPR017942; Lipid-bd_serum_glycop_N.
DR InterPro; IPR001233; RtcB.
DR InterPro; IPR036025; RtcB-like_sf.
DR InterPro; IPR027513; RtcB_euk.
DR PANTHER; PTHR11118:SF1; RNA-SPLICING LIGASE RTCB HOMOLOG; 1.
DR PANTHER; PTHR11118; UNCHARACTERIZED; 1.
DR Pfam; PF01273; LBP_BPI_CETP; 1.
DR Pfam; PF02886; LBP_BPI_CETP_C; 1.
DR Pfam; PF01139; RtcB; 1.
DR SMART; SM00328; BPI1; 1.
DR SMART; SM00329; BPI2; 1.
DR SUPFAM; SSF55394; Bactericidal permeability-increasing protein, BPI; 2.
DR SUPFAM; SSF103365; Hypothetical protein PH1602; 1.
DR PROSITE; PS01288; UPF0027; 1.
PE 3: Inferred from homology;
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_03144};
KW GTP-binding {ECO:0000256|ARBA:ARBA00023134, ECO:0000256|HAMAP-
KW Rule:MF_03144};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_03144};
KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|HAMAP-Rule:MF_03144};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_03144};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_03144}; Reference proteome {ECO:0000313|Proteomes:UP000030684};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_03144}.
FT DOMAIN 1..211
FT /note="Lipid-binding serum glycoprotein N-terminal"
FT /evidence="ECO:0000259|SMART:SM00328"
FT DOMAIN 226..406
FT /note="Lipid-binding serum glycoprotein C-terminal"
FT /evidence="ECO:0000259|SMART:SM00329"
FT ACT_SITE 817
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-1"
FT BINDING 508
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-3"
FT BINDING 511
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144"
FT BINDING 511
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144"
FT BINDING 615..619
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-2"
FT BINDING 616
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-3"
FT BINDING 648
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-3"
FT BINDING 742..743
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-2"
FT BINDING 742
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-3"
FT BINDING 791..794
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-2"
FT BINDING 798
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-2"
FT BINDING 817..820
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-2"
FT BINDING 893
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-2"
SQ SEQUENCE 894 AA; 98311 MW; 10B719B166D84874 CRC64;
MEIIEQMVKE RNISDLKGSE SLEFLKIDYV NYNFTNIKIT AFSFPNTSLA FVPGVGIRAL
TNHGIANIST DWDIKSPLFQ DTGGADLFLS EVYFTGILIL SRNNFGHPVL KLQDCYAQVS
HADVSFSGEF SVLYNSFAEP MEKPILKNLN EMLCPIIIHE VEALNANLSM LQVFTKIDNY
TLLDYSLISS PEITENYIEL NLKGVFYPQE NLADPPFPSV PFVLPEGSDS MLYIGISKYF
FKSASYAYFT AGAFGVTLTT KEIAELYILS QPFMVQVMAT EPPVINLLPG NFTLDIPASI
MILTQSKNST AETIVSMDFV ASTSVGLVIL GQRLICSLSL NRFRLSLPES NRSNIEVLRF
ENILSSILHF GVLPLANAKP GVFATVVTAM SRSYNDELQF LEKINKNCWR IKKGFVPNMQ
VEGVFYVNDA LEKLMFEELR NACRGGGVGG FLPAMKQIGN VAALPGIVHR SIGLPDVHSG
YGFAIGNMAA FDMNDPEAVV SPGGVGFDIN CGVRLLRTNL DESDVQPVKE QLAQAMFDHI
PVGVGSKGVI PMNAKDLEEA LEMGVDWSLR EGYAWAEDKE HCEEYGRMLQ ADPNKVSARA
KKRGLPQLGT LGAGNHYAEI QVVDEIFNEY AAKKMGIDHK GQVCVMIHSG SRGLGHQVAT
DALVAMEKAM KRDKIIVNDR QLACARIASP EGQDYLKGMA AAGNYAWVNR SSMTFLTRQA
FAKVFNTTPD DLDLHVIYDV SHNIAKVEQH VVDGKERTLL VHRKGSTRAF PPHHPLIAVD
YQLTGQPVLI GGTMGTCSYV LTGTEQGMTE TFGTTCHGAG RALSRAKSRR NLDFQDVLDK
LADMGIAIRV ASPKLVMEEA PESYKNVTDV VNTCHDAGIS KKTIKLRPIA VIKG
//
