RTCB_MOUSE
ID RTCB_MOUSE Reviewed; 505 AA.
AC Q99LF4; Q3TA04; Q3TI25; Q3UDW6;
DT 31-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=RNA-splicing ligase RtcB homolog {ECO:0000255|HAMAP-Rule:MF_03144};
DE EC=6.5.1.8 {ECO:0000255|HAMAP-Rule:MF_03144};
DE AltName: Full=3'-phosphate/5'-hydroxy nucleic acid ligase {ECO:0000255|HAMAP-Rule:MF_03144};
DE AltName: Full=Focal adhesion-associated protein;
DE Short=FAAP;
GN Name=Rtcb {ECO:0000255|HAMAP-Rule:MF_03144}; Synonyms=D10Wsu52e;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND SUBCELLULAR LOCATION.
RC STRAIN=BALB/cJ;
RX PubMed=18508721; DOI=10.2741/3215;
RA Hu J., Teng J., Ding N., He M., Sun Y., Yu A.C., Chen J.;
RT "FAAP, a novel murine protein, is involved in cell adhesion through
RT regulating vinculin-paxillin association.";
RL Front. Biosci. 13:7123-7131(2008).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J, DBA/2J, and NOD;
RC TISSUE=Embryo, Macrophage, Placenta, and Spleen;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=FVB/N; TISSUE=Mammary tumor;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP FUNCTION.
RX PubMed=20510672; DOI=10.1016/j.bbrc.2010.05.105;
RA Wang Y., Hai T., Liu Z., Zhou S., Lv Z., Ding C., Liu L., Niu Y., Zhao X.,
RA Tong M., Wang L., Jouneau A., Zhang X., Ji W., Zhou Q.;
RT "HSPC117 deficiency in cloned embryos causes placental abnormality and
RT fetal death.";
RL Biochem. Biophys. Res. Commun. 397:407-412(2010).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas,
RC Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [6]
RP TISSUE SPECIFICITY, AND INDUCTION.
RX PubMed=21046479; DOI=10.1007/s12020-010-9371-z;
RA Ding N.Z., He M., He C.Q., Hu J.S., Teng J., Chen J.;
RT "Expression and regulation of FAAP in the mouse epididymis.";
RL Endocrine 38:188-193(2010).
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 (By similarity). Essential during post-implantation development of
CC embryos. {ECO:0000255|HAMAP-Rule:MF_03144,
CC ECO:0000269|PubMed:20510672}.
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:0000255|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:0000255|HAMAP-Rule:MF_03144};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03144};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_03144};
CC -!- SUBUNIT: Catalytic component of the tRNA-splicing ligase complex.
CC {ECO:0000255|HAMAP-Rule:MF_03144}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Cytoplasm
CC {ECO:0000255|HAMAP-Rule:MF_03144, ECO:0000269|PubMed:18508721}.
CC Note=Enters into the nucleus in case of active transcription while it
CC accumulates in cytosol when transcription level is low. {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Ubiquitously expressed. Highly expressed in the
CC epididymis with predominant enrichment in the initial segment. During
CC sexual maturation, it is expressed in the caput epididymides.
CC {ECO:0000269|PubMed:21046479}.
CC -!- INDUCTION: Down-regulated in the epididymis upon castration.
CC {ECO:0000269|PubMed:21046479}.
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:0000255|HAMAP-Rule:MF_03144}.
CC -!- SIMILARITY: Belongs to the RtcB family. {ECO:0000255|HAMAP-
CC Rule:MF_03144}.
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DR EMBL; AY424364; AAR02005.1; -; mRNA.
DR EMBL; AK145891; BAE26729.1; -; mRNA.
DR EMBL; AK145916; BAE26747.1; -; mRNA.
DR EMBL; AK149885; BAE29145.1; -; mRNA.
DR EMBL; AK150376; BAE29508.1; -; mRNA.
DR EMBL; AK150470; BAE29587.1; -; mRNA.
DR EMBL; AK151042; BAE30059.1; -; mRNA.
DR EMBL; AK151182; BAE30183.1; -; mRNA.
DR EMBL; AK151932; BAE30808.1; -; mRNA.
DR EMBL; AK152144; BAE30981.1; -; mRNA.
DR EMBL; AK153434; BAE31991.1; -; mRNA.
DR EMBL; AK168038; BAE40021.1; -; mRNA.
DR EMBL; AK172175; BAE42866.1; -; mRNA.
DR EMBL; BC003288; AAH03288.1; -; mRNA.
DR CCDS; CCDS24094.1; -.
DR RefSeq; NP_663397.1; NM_145422.4.
DR AlphaFoldDB; Q99LF4; -.
DR SMR; Q99LF4; -.
DR BioGRID; 205756; 22.
DR IntAct; Q99LF4; 7.
DR MINT; Q99LF4; -.
DR STRING; 10090.ENSMUSP00000001834; -.
DR iPTMnet; Q99LF4; -.
DR PhosphoSitePlus; Q99LF4; -.
DR SwissPalm; Q99LF4; -.
DR EPD; Q99LF4; -.
DR jPOST; Q99LF4; -.
DR MaxQB; Q99LF4; -.
DR PaxDb; Q99LF4; -.
DR PeptideAtlas; Q99LF4; -.
DR PRIDE; Q99LF4; -.
DR ProteomicsDB; 256798; -.
DR Antibodypedia; 261; 230 antibodies from 29 providers.
DR DNASU; 28088; -.
DR Ensembl; ENSMUST00000001834; ENSMUSP00000001834; ENSMUSG00000001783.
DR GeneID; 28088; -.
DR KEGG; mmu:28088; -.
DR UCSC; uc007gni.1; mouse.
DR CTD; 51493; -.
DR MGI; MGI:106379; Rtcb.
DR VEuPathDB; HostDB:ENSMUSG00000001783; -.
DR eggNOG; KOG3833; Eukaryota.
DR GeneTree; ENSGT00940000155911; -.
DR HOGENOM; CLU_022279_0_0_1; -.
DR InParanoid; Q99LF4; -.
DR OMA; QTRGVEC; -.
DR OrthoDB; 394775at2759; -.
DR PhylomeDB; Q99LF4; -.
DR TreeFam; TF314404; -.
DR BRENDA; 6.5.1.8; 3474.
DR BioGRID-ORCS; 28088; 27 hits in 74 CRISPR screens.
DR ChiTaRS; Rtcb; mouse.
DR PRO; PR:Q99LF4; -.
DR Proteomes; UP000000589; Chromosome 10.
DR RNAct; Q99LF4; protein.
DR Bgee; ENSMUSG00000001783; Expressed in urogenital fold and 260 other tissues.
DR Genevisible; Q99LF4; MM.
DR GO; GO:0005737; C:cytoplasm; IDA:MGI.
DR GO; GO:0005829; C:cytosol; ISO:MGI.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IDA:WormBase.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; ISO:MGI.
DR GO; GO:0005635; C:nuclear envelope; IDA:WormBase.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0072669; C:tRNA-splicing ligase complex; ISS:UniProtKB.
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; ISS:UniProtKB.
DR GO; GO:0017166; F:vinculin binding; ISO:MGI.
DR GO; GO:0001701; P:in utero embryonic development; IMP:MGI.
DR GO; GO:0001890; P:placenta development; IMP:MGI.
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; ISS:UniProtKB.
DR Gene3D; 3.90.1860.10; -; 1.
DR HAMAP; MF_03144; RtcB_euk; 1.
DR InterPro; IPR001233; RtcB.
DR InterPro; IPR036025; RtcB-like_sf.
DR InterPro; IPR027513; RtcB_euk.
DR PANTHER; PTHR11118; PTHR11118; 1.
DR Pfam; PF01139; RtcB; 1.
DR SUPFAM; SSF103365; SSF103365; 1.
DR PROSITE; PS01288; UPF0027; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; GTP-binding; Isopeptide bond; Ligase; Manganese; Metal-binding;
KW Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
KW tRNA processing; Ubl conjugation.
FT CHAIN 1..505
FT /note="RNA-splicing ligase RtcB homolog"
FT /id="PRO_0000255243"
FT ACT_SITE 428
FT /note="GMP-histidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 119
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 122
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 122
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 226..230
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 227
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 259
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 353..354
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 353
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 402..405
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 409
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 428..431
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT BINDING 504
FT /ligand="GMP"
FT /ligand_id="ChEBI:CHEBI:58115"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03144"
FT MOD_RES 300
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9Y3I0"
FT CROSSLNK 496
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q9Y3I0"
FT CONFLICT 30
FT /note="M -> V (in Ref. 2; BAE42866)"
FT /evidence="ECO:0000305"
FT CONFLICT 125
FT /note="R -> H (in Ref. 2; BAE42866)"
FT /evidence="ECO:0000305"
FT CONFLICT 165
FT /note="A -> V (in Ref. 2; BAE40021)"
FT /evidence="ECO:0000305"
FT CONFLICT 178
FT /note="W -> R (in Ref. 2; BAE29145)"
FT /evidence="ECO:0000305"
FT CONFLICT 205
FT /note="N -> S (in Ref. 2; BAE42866)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 505 AA; 55249 MW; 3488A9BF91460480 CRC64;
MSRNYNDELQ FLDKINKNCW RIKKGFVPNM QVEGVFYVND ALEKLMFEEL RNACRGGGVG
GFLPAMKQIG NVAALPGIVH RSIGLPDVHS GYGFAIGNMA AFDMNDPEAV VSPGGVGFDI
NCGVRLLRTN LDESDVQPVK EQLAQAMFDH IPVGVGSKGV IPMNAKDLEE ALEMGVDWSL
REGYAWAEDK EHCEEYGRML QADPNKVSPR AKKRGLPQLG TLGAGNHYAE IQVVDEIFNE
YAAKKMGIDH KGQVCVMIHS GSRGLGHQVA TDALVAMEKA MKRDKIIVND RQLACARIAS
PEGQDYLKGM AAAGNYAWVN RSSMTFLTRQ AFAKVFNTTP DDLDLHVIYD VSHNIAKVEQ
HVVDGKERTL LVHRKGSTRA FPPHHPLIAV DYQLTGQPVL IGGTMGTCSY VLTGTEQGMT
ETFGTTCHGA GRALSRAKSR RNLDFQDVLD KLADMGIAIR VASPKLVMEE APESYKNVTD
VVNTCHDAGI SKKAIKLRPI AVIKG
