URM1_MOUSE
ID URM1_MOUSE Reviewed; 101 AA.
AC Q9D2P4; A3KGW2; Q8BHY9;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Ubiquitin-related modifier 1 {ECO:0000255|HAMAP-Rule:MF_03048};
GN Name=Urm1;
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=Hippocampus;
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 [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Eye;
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, 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 STRUCTURE BY NMR.
RG RIKEN structural genomics initiative (RSGI);
RT "Solution structure of mouse hypothetical protein 2900073H19RIK.";
RL Submitted (MAY-2004) to the PDB data bank.
RN [7]
RP STRUCTURE BY NMR OF 2-101.
RX PubMed=16046629; DOI=10.1110/ps.051577605;
RA Singh S., Tonelli M., Tyler R.C., Bahrami A., Lee M.S., Markley J.L.;
RT "Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a
RT putative eukaryotic Urm1.";
RL Protein Sci. 14:2095-2102(2005).
CC -!- FUNCTION: Acts as a sulfur carrier required for 2-thiolation of
CC mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu)
CC and tRNA(Gln). Serves as sulfur donor in tRNA 2-thiolation reaction by
CC being thiocarboxylated (-COSH) at its C-terminus by MOCS3. The sulfur
CC is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Also
CC acts as a ubiquitin-like protein (UBL) that is covalently conjugated
CC via an isopeptide bond to lysine residues of target proteins such as
CC MOCS3, ATPBD3, CTU2, USP15 and CAS. The thiocarboxylated form serves as
CC substrate for conjugation and oxidative stress specifically induces the
CC formation of UBL-protein conjugates. {ECO:0000255|HAMAP-Rule:MF_03048}.
CC -!- PATHWAY: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA
CC biosynthesis. {ECO:0000255|HAMAP-Rule:MF_03048}.
CC -!- SUBUNIT: Component of a complex at least composed of URM1, CTU2/NCS2
CC and CTU1/ATPBD3. {ECO:0000255|HAMAP-Rule:MF_03048}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_03048}.
CC -!- PTM: C-terminal thiocarboxylation occurs in 2 steps, it is first acyl-
CC adenylated (-COAMP) via the hesA/moeB/thiF part of MOCS3, then
CC thiocarboxylated (-COSH) via the rhodanese domain of MOCS3.
CC {ECO:0000255|HAMAP-Rule:MF_03048}.
CC -!- SIMILARITY: Belongs to the URM1 family. {ECO:0000255|HAMAP-
CC Rule:MF_03048}.
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DR EMBL; AK019352; BAB31673.1; -; mRNA.
DR EMBL; AK049227; BAC33621.1; -; mRNA.
DR EMBL; AK049849; BAC33956.1; -; mRNA.
DR EMBL; AL928926; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH466542; EDL08423.1; -; Genomic_DNA.
DR EMBL; BC026994; AAH26994.1; -; mRNA.
DR CCDS; CCDS15859.1; -.
DR RefSeq; NP_080891.1; NM_026615.4.
DR PDB; 1WGK; NMR; -; A=1-101.
DR PDB; 1XO3; NMR; -; A=2-101.
DR PDBsum; 1WGK; -.
DR PDBsum; 1XO3; -.
DR AlphaFoldDB; Q9D2P4; -.
DR BMRB; Q9D2P4; -.
DR SMR; Q9D2P4; -.
DR BioGRID; 212728; 4.
DR STRING; 10090.ENSMUSP00000088676; -.
DR iPTMnet; Q9D2P4; -.
DR PhosphoSitePlus; Q9D2P4; -.
DR EPD; Q9D2P4; -.
DR MaxQB; Q9D2P4; -.
DR PaxDb; Q9D2P4; -.
DR PeptideAtlas; Q9D2P4; -.
DR PRIDE; Q9D2P4; -.
DR ProteomicsDB; 299645; -.
DR Antibodypedia; 17464; 131 antibodies from 27 providers.
DR DNASU; 68205; -.
DR Ensembl; ENSMUST00000091142; ENSMUSP00000088676; ENSMUSG00000069020.
DR GeneID; 68205; -.
DR KEGG; mmu:68205; -.
DR UCSC; uc008jag.1; mouse.
DR CTD; 81605; -.
DR MGI; MGI:1915455; Urm1.
DR VEuPathDB; HostDB:ENSMUSG00000069020; -.
DR eggNOG; KOG4146; Eukaryota.
DR GeneTree; ENSGT00390000005101; -.
DR HOGENOM; CLU_148208_0_1_1; -.
DR InParanoid; Q9D2P4; -.
DR OMA; DYELQPN; -.
DR OrthoDB; 1541629at2759; -.
DR PhylomeDB; Q9D2P4; -.
DR TreeFam; TF336363; -.
DR UniPathway; UPA00988; -.
DR BioGRID-ORCS; 68205; 23 hits in 73 CRISPR screens.
DR ChiTaRS; Urm1; mouse.
DR EvolutionaryTrace; Q9D2P4; -.
DR PRO; PR:Q9D2P4; -.
DR Proteomes; UP000000589; Chromosome 2.
DR RNAct; Q9D2P4; protein.
DR Bgee; ENSMUSG00000069020; Expressed in yolk sac and 247 other tissues.
DR Genevisible; Q9D2P4; MM.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-UniRule.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0031386; F:protein tag; IBA:GO_Central.
DR GO; GO:0097163; F:sulfur carrier activity; ISO:MGI.
DR GO; GO:0032447; P:protein urmylation; IBA:GO_Central.
DR GO; GO:0034227; P:tRNA thio-modification; ISS:UniProtKB.
DR GO; GO:0002098; P:tRNA wobble uridine modification; ISS:UniProtKB.
DR CDD; cd01764; Ubl_Urm1; 1.
DR Gene3D; 3.10.20.30; -; 1.
DR HAMAP; MF_03048; Urm1; 1.
DR InterPro; IPR012675; Beta-grasp_dom_sf.
DR InterPro; IPR016155; Mopterin_synth/thiamin_S_b.
DR InterPro; IPR015221; Urm1.
DR PANTHER; PTHR14986; PTHR14986; 1.
DR Pfam; PF09138; Urm1; 1.
DR PIRSF; PIRSF037379; Ubiquitin-related_modifier_1; 1.
DR SUPFAM; SSF54285; SSF54285; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Isopeptide bond; Reference proteome;
KW tRNA processing; Ubl conjugation pathway.
FT CHAIN 1..101
FT /note="Ubiquitin-related modifier 1"
FT /id="PRO_0000089715"
FT MOD_RES 101
FT /note="1-thioglycine; alternate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03048"
FT CROSSLNK 101
FT /note="Glycyl lysine isopeptide (Gly-Lys) (interchain with
FT K-? in acceptor proteins); alternate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03048"
FT CONFLICT 31
FT /note="G -> R (in Ref. 1; BAC33621)"
FT /evidence="ECO:0000305"
FT STRAND 5..11
FT /evidence="ECO:0007829|PDB:1WGK"
FT TURN 13..15
FT /evidence="ECO:0007829|PDB:1WGK"
FT HELIX 16..18
FT /evidence="ECO:0007829|PDB:1WGK"
FT TURN 19..21
FT /evidence="ECO:0007829|PDB:1WGK"
FT STRAND 23..29
FT /evidence="ECO:0007829|PDB:1WGK"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:1XO3"
FT HELIX 38..45
FT /evidence="ECO:0007829|PDB:1WGK"
FT TURN 46..49
FT /evidence="ECO:0007829|PDB:1WGK"
FT HELIX 54..57
FT /evidence="ECO:0007829|PDB:1WGK"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:1WGK"
FT STRAND 65..75
FT /evidence="ECO:0007829|PDB:1WGK"
FT HELIX 76..79
FT /evidence="ECO:0007829|PDB:1WGK"
FT TURN 81..83
FT /evidence="ECO:0007829|PDB:1WGK"
FT STRAND 88..96
FT /evidence="ECO:0007829|PDB:1WGK"
SQ SEQUENCE 101 AA; 11323 MW; 535D437F0D32929E CRC64;
MAAPLCVKVE FGGGAELLFD GVKKHQVALP GQEEPWDIRN LLVWIKKNLL KERPELFIQG
DSVRPGILVL INDADWELLG ELDYQLQDQD SILFISTLHG G
