YRDC_MOUSE
ID YRDC_MOUSE Reviewed; 280 AA.
AC Q3U5F4; B1ARW9; B1ARX2; Q7TSY0; Q8CII1;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2005, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Threonylcarbamoyl-AMP synthase {ECO:0000305};
DE EC=2.7.7.87 {ECO:0000250|UniProtKB:Q86U90};
DE AltName: Full=Ischemia/reperfusion-inducible protein {ECO:0000303|PubMed:16024787};
DE Short=mIRIP {ECO:0000303|PubMed:16024787};
DE Flags: Precursor;
GN Name=Yrdc; Synonyms=Irip {ECO:0000303|PubMed:16024787};
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 [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Thymus;
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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 4-280, FUNCTION, SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, INDUCTION, AND INTERACTION WITH RSC1A1.
RC STRAIN=C57BL/6 X CBA; TISSUE=Kidney;
RX PubMed=16024787; DOI=10.1128/mcb.25.15.6496-6508.2005;
RA Jiang W., Prokopenko O., Wong L., Inouye M., Mirochnitchenko O.;
RT "IRIP, a new ischemia/reperfusion-inducible protein that participates in
RT the regulation of transporter activity.";
RL Mol. Cell. Biol. 25:6496-6508(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 4-280.
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 [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Heart, Pancreas, 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 IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, and Embryo;
RX PubMed=24129315; DOI=10.1074/mcp.o113.027870;
RA Guo A., Gu H., Zhou J., Mulhern D., Wang Y., Lee K.A., Yang V., Aguiar M.,
RA Kornhauser J., Jia X., Ren J., Beausoleil S.A., Silva J.C., Vemulapalli V.,
RA Bedford M.T., Comb M.J.;
RT "Immunoaffinity enrichment and mass spectrometry analysis of protein
RT methylation.";
RL Mol. Cell. Proteomics 13:372-387(2014).
CC -!- FUNCTION: Cytoplasmic and mitochondrial threonylcarbamoyl-AMP synthase
CC required for the formation of a threonylcarbamoyl group on adenosine at
CC position 37 (t(6)A37) in tRNAs that read codons beginning with adenine.
CC Catalyzes the conversion of L-threonine, HCO(3)(-)/CO(2) and ATP to
CC give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate,
CC with the release of diphosphate. Participates in t(6)A37 formation in
CC cytoplasmic and mitochondrial tRNAs (By similarity). May regulate the
CC activity of some transporters (PubMed:16024787).
CC {ECO:0000250|UniProtKB:Q86U90, ECO:0000269|PubMed:16024787}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + hydrogencarbonate + L-threonine = diphosphate + H2O + L-
CC threonylcarbamoyladenylate; Xref=Rhea:RHEA:36407, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:17544, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:57926, ChEBI:CHEBI:73682; EC=2.7.7.87;
CC Evidence={ECO:0000250|UniProtKB:Q86U90};
CC -!- SUBUNIT: Interacts with RSC1A1. {ECO:0000269|PubMed:16024787}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q86U90}.
CC Mitochondrion {ECO:0000250|UniProtKB:Q86U90}. Cell membrane
CC {ECO:0000269|PubMed:16024787}; Peripheral membrane protein
CC {ECO:0000269|PubMed:16024787}. Note=A large fraction localizes in the
CC cytoplasm, whereas a smaller fraction is imported to mitochondria.
CC {ECO:0000250|UniProtKB:Q86U90}.
CC -!- TISSUE SPECIFICITY: Widely expressed. Expressed at higher level in
CC testis, secretory, and endocrine organs. {ECO:0000269|PubMed:16024787}.
CC -!- INDUCTION: By ischemia/reperfusion and endotoxemia.
CC {ECO:0000269|PubMed:16024787}.
CC -!- DOMAIN: The mitochondrial targeting sequence (MTS) is weak and only
CC mediates import of a small fraction of YRDC in mitochondria.
CC {ECO:0000250|UniProtKB:Q86U90}.
CC -!- SIMILARITY: Belongs to the SUA5 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH23823.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=AAP37032.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CAM16101.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CAP19076.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AK153627; BAE32125.1; -; mRNA.
DR EMBL; AL606933; CAM16101.1; ALT_INIT; Genomic_DNA.
DR EMBL; AL606933; CAP19076.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AY283537; AAP37032.1; ALT_INIT; mRNA.
DR EMBL; BC023823; AAH23823.1; ALT_INIT; mRNA.
DR CCDS; CCDS18628.2; -.
DR RefSeq; NP_705794.2; NM_153566.2.
DR AlphaFoldDB; Q3U5F4; -.
DR SMR; Q3U5F4; -.
DR BioGRID; 231008; 1.
DR STRING; 10090.ENSMUSP00000099688; -.
DR iPTMnet; Q3U5F4; -.
DR PhosphoSitePlus; Q3U5F4; -.
DR EPD; Q3U5F4; -.
DR MaxQB; Q3U5F4; -.
DR PaxDb; Q3U5F4; -.
DR PeptideAtlas; Q3U5F4; -.
DR PRIDE; Q3U5F4; -.
DR ProteomicsDB; 275230; -.
DR Antibodypedia; 31792; 26 antibodies from 13 providers.
DR Ensembl; ENSMUST00000102628; ENSMUSP00000099688; ENSMUSG00000028889.
DR GeneID; 230734; -.
DR KEGG; mmu:230734; -.
DR UCSC; uc008urf.2; mouse.
DR CTD; 79693; -.
DR MGI; MGI:2387201; Yrdc.
DR VEuPathDB; HostDB:ENSMUSG00000028889; -.
DR eggNOG; KOG3051; Eukaryota.
DR GeneTree; ENSGT00390000015364; -.
DR HOGENOM; CLU_031397_5_1_1; -.
DR InParanoid; Q3U5F4; -.
DR OMA; LVDAFWP; -.
DR OrthoDB; 1027994at2759; -.
DR PhylomeDB; Q3U5F4; -.
DR TreeFam; TF314358; -.
DR BioGRID-ORCS; 230734; 27 hits in 72 CRISPR screens.
DR ChiTaRS; Yrdc; mouse.
DR PRO; PR:Q3U5F4; -.
DR Proteomes; UP000000589; Chromosome 4.
DR RNAct; Q3U5F4; protein.
DR Bgee; ENSMUSG00000028889; Expressed in ectoplacental cone and 62 other tissues.
DR ExpressionAtlas; Q3U5F4; baseline and differential.
DR Genevisible; Q3U5F4; MM.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0016020; C:membrane; IDA:MGI.
DR GO; GO:0005739; C:mitochondrion; ISS:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0003725; F:double-stranded RNA binding; IEA:InterPro.
DR GO; GO:0061710; F:L-threonylcarbamoyladenylate synthase; ISS:UniProtKB.
DR GO; GO:0016779; F:nucleotidyltransferase activity; IBA:GO_Central.
DR GO; GO:0000049; F:tRNA binding; IBA:GO_Central.
DR GO; GO:0051051; P:negative regulation of transport; ISO:MGI.
DR GO; GO:0006450; P:regulation of translational fidelity; IBA:GO_Central.
DR GO; GO:0002949; P:tRNA threonylcarbamoyladenosine modification; ISS:UniProtKB.
DR InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR InterPro; IPR006070; YrdC-like_dom.
DR Pfam; PF01300; Sua5_yciO_yrdC; 1.
DR SUPFAM; SSF55821; SSF55821; 1.
DR TIGRFAMs; TIGR00057; TIGR00057; 1.
DR PROSITE; PS51163; YRDC; 1.
PE 1: Evidence at protein level;
KW Cell membrane; Cytoplasm; Membrane; Mitochondrion; Phosphoprotein;
KW Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..56
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 57..280
FT /note="Threonylcarbamoyl-AMP synthase"
FT /id="PRO_0000341403"
FT DOMAIN 68..258
FT /note="YrdC-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00518"
FT MOD_RES 61
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q86U90"
FT CONFLICT 35
FT /note="R -> L (in Ref. 3; AAP37032)"
FT /evidence="ECO:0000305"
FT CONFLICT 65
FT /note="S -> A (in Ref. 3; AAP37032 and 4; AAH23823)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 280 AA; 29454 MW; 77DA9573081725F0 CRC64;
MSTARPCAGL RAAVAAGMGL SDGPASSGRG CRLLRPPEPA PALPGARLLR LPESEPVEAA
SPERSGWTEA LRAAVAELRA GAVVAVPTDT LYGLACSASS SAALSCVYRL KGRSEAKPLA
VCLGRVADVY RYCQVRVPRE LLEDLFPGPV TLVMERSEEL NKDLNPFTRL VGIRIPDHAF
MLDLAQMFGG PLALTSANLS SQASSLSVEE FQDLWPHLSL VIDGGPIGDS QSPECRLGST
VVDLSVPGKF GIIRPGCALE NTTSILQQKY GLLPSQGSCS
