ID A0A158QZI0_NIPBR Unreviewed; 1016 AA.
AC A0A158QZI0;
DT 08-JUN-2016, integrated into UniProtKB/TrEMBL.
DT 08-JUN-2016, sequence version 1.
DT 27-MAR-2024, entry version 33.
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 ORFNames=NBR_LOCUS10168 {ECO:0000313|EMBL:VDL73757.1};
OS Nippostrongylus brasiliensis (Rat hookworm).
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Strongyloidea; Heligmosomidae; Nippostrongylus.
OX NCBI_TaxID=27835 {ECO:0000313|Proteomes:UP000038043, ECO:0000313|WBParaSite:NBR_0001016701-mRNA-1};
RN [1] {ECO:0000313|WBParaSite:NBR_0001016701-mRNA-1}
RP IDENTIFICATION.
RG WormBaseParasite;
RL Submitted (APR-2016) to UniProtKB.
RN [2] {ECO:0000313|EMBL:VDL73757.1, ECO:0000313|Proteomes:UP000271162}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RG Pathogen Informatics;
RL Submitted (NOV-2018) to the EMBL/GenBank/DDBJ databases.
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 -!- 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; UYSL01020264; VDL73757.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A158QZI0; -.
DR STRING; 27835.A0A158QZI0; -.
DR WBParaSite; NBR_0001016701-mRNA-1; NBR_0001016701-mRNA-1; NBR_0001016701.
DR Proteomes; UP000038043; Unplaced.
DR Proteomes; UP000271162; Unassembled WGS sequence.
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: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 CDD; cd12883; SPRY_RING; 1.
DR Gene3D; 2.60.120.920; -; 1.
DR Gene3D; 3.90.1860.10; tRNA-splicing ligase RtcB; 1.
DR HAMAP; MF_03144; RtcB_euk; 1.
DR InterPro; IPR001870; B30.2/SPRY.
DR InterPro; IPR043136; B30.2/SPRY_sf.
DR InterPro; IPR013320; ConA-like_dom_sf.
DR InterPro; IPR001233; RtcB.
DR InterPro; IPR036025; RtcB-like_sf.
DR InterPro; IPR027513; RtcB_euk.
DR InterPro; IPR003877; SPRY_dom.
DR InterPro; IPR035774; SPRY_RSPRY1.
DR PANTHER; PTHR11118:SF1; RNA-SPLICING LIGASE RTCB HOMOLOG; 1.
DR PANTHER; PTHR11118; UNCHARACTERIZED; 1.
DR Pfam; PF01139; RtcB; 1.
DR Pfam; PF00622; SPRY; 1.
DR SMART; SM00449; SPRY; 1.
DR SUPFAM; SSF49899; Concanavalin A-like lectins/glucanases; 1.
DR SUPFAM; SSF103365; Hypothetical protein PH1602; 1.
DR PROSITE; PS50188; B302_SPRY; 1.
PE 3: Inferred from homology;
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:UP000271162};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_03144}.
FT DOMAIN 274..460
FT /note="B30.2/SPRY"
FT /evidence="ECO:0000259|PROSITE:PS50188"
FT REGION 25..49
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 25..43
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 939
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144,
FT ECO:0000256|PIRSR:PIRSR601233-1"
FT BINDING 630
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 633
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144"
FT BINDING 633
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_03144"
FT BINDING 737..741
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 738
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 770
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 864..865
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 864
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 913..916
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 920
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 939..942
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 1015
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 1016 AA; 113020 MW; D7BBEA116129F5E7 CRC64;
MSRLAGCNCM LATFLQSFHI DSRNPRGCRR NDERNRSPQS FDQDVDFETE GSSQLGRRMS
MTNYVGNDVK DLIRQTLKVI RSLVNNEQDP PASLLKLNMI AEREKGWLLV VESLIETVPD
DDSLGPAVIT LFLDECPLPS KDTVHRLLCS LRLDLASSSS TTRKRSWHRN TCIVLGSLAE
KLAGSSSVAM CNPTTLNYLI SRILPPFTQA RVVLFALLAL EKFAQTSENQ FLISRTLEES
ATHPLKQLEE WRHCTSNAMK RQVGFCATWA LDNIFITPNR IYAYETTNVS NINAMLNHED
VSEYLKIGPD GLEARCDVSS FESVRCTFAV QDGVWFYEAT VFTPGVMQIG FATKRSRFLN
HEGYGIGDDE SSVAYDGCRQ LLWHNANSSR HEHEPWSPGD VVGCLLNIPL GTVMFYLNGR
PLQRPHLEFL RNRPAGDGVF AAASFMSFQQ CRFNFGAEPF KYPPDIAFST FNDGGATLTT
EQKTILPRRR RLELLQKEPI PEDYCTICYA NPGDTLLEPC MHGMPRTFEE ECAFIERVSE
CKFKIKKGFV PNMNVECRFY VNKKLEQQMF EELRLSIGRL GNVAALPGIV GHSIGLPDIH
SGYGFSIGNI AAFDCSNKDS VISPGGVGFD INCGVRLIRT NLFERDVQPV KEQLAQALFD
YIPVGVGSRG AIPMSASDLV DCLEMGMDWT LREGYSWAED KEHCEEYGRM LQADATKVST
RAKKRGLPQL GTLGAGNHYA EVQVVDEIFD KHAASKMGIG ELGQVVVMLH CGSRGLGHQV
ATDALVEMEK AMARDGIVVN DRQLACARLN STEGQDYLKG MAAAANFAWV NRSCMTFCVR
QAFANVFTMQ PDDLDMQMIY DVSHNVAKME EHLVDGRPTQ LCVHRKGATR AFPPHHPLIP
IDYQLTGQPV LIGGSMGTCS YVLTGTERGM VEAYGTTCHG AGRALSRSKS RQKIPWTDVI
ENLKQKGISI RLASPKLIME EAPESYKDVT DVVNTCDMAG ISKKAVKLRP IAVIKG
//
