URM1_HUMAN
ID URM1_HUMAN Reviewed; 101 AA.
AC Q9BTM9; B3KMH3; B4DV08; Q5T4B4;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Ubiquitin-related modifier 1 {ECO:0000255|HAMAP-Rule:MF_03048};
GN Name=URM1 {ECO:0000255|HAMAP-Rule:MF_03048}; Synonyms=C9orf74;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Placenta, and Small intestine;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15164053; DOI=10.1038/nature02465;
RA Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L.,
RA Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R.,
RA Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S.,
RA Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K.,
RA Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y.,
RA Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C.,
RA Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E.,
RA Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M.,
RA Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J.,
RA Frankish A., Frankland J.A., French L., Fricker D.G., Garner P.,
RA Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S.,
RA Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E.,
RA Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D.,
RA Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E.,
RA Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K.,
RA Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S.,
RA Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J.,
RA Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E.,
RA McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V.,
RA Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S.,
RA Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K.,
RA Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J.,
RA Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M.,
RA West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L.,
RA Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M.,
RA Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J.,
RA Dunham I.;
RT "DNA sequence and analysis of human chromosome 9.";
RL Nature 429:369-374(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Placenta;
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 FUNCTION IN 2-THIOLATION OF TRNA, IDENTIFICATION IN A COMPLEX WITH CTU1 AND
RP C16ORF84, AND THIOCARBOXYLATION AT GLY-101.
RX PubMed=19017811; DOI=10.1073/pnas.0808756105;
RA Schlieker C.D., Van der Veen A.G., Damon J.R., Spooner E., Ploegh H.L.;
RT "A functional proteomics approach links the ubiquitin-related modifier Urm1
RT to a tRNA modification pathway.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:18255-18260(2008).
RN [6]
RP FUNCTION IN PROTEIN CONJUGATION, AND IDENTIFICATION OF SUBSTRATES.
RX PubMed=21209336; DOI=10.1073/pnas.1014402108;
RA Van der Veen A.G., Schorpp K., Schlieker C., Buti L., Damon J.R.,
RA Spooner E., Ploegh H.L., Jentsch S.;
RT "Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed
RT protein modifier.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:1763-1770(2011).
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 ECO:0000269|PubMed:19017811, ECO:0000269|PubMed:21209336}.
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 ECO:0000269|PubMed:19017811}.
CC -!- INTERACTION:
CC Q9BTM9; P55060: CSE1L; NbExp=2; IntAct=EBI-714589, EBI-286709;
CC Q9BTM9; Q7Z7A3: CTU1; NbExp=7; IntAct=EBI-714589, EBI-15741880;
CC Q9BTM9; O95396: MOCS3; NbExp=4; IntAct=EBI-714589, EBI-373206;
CC Q9BTM9; Q9Y4E8: USP15; NbExp=2; IntAct=EBI-714589, EBI-1043104;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q9BTM9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9BTM9-2; Sequence=VSP_040026;
CC Name=3;
CC IsoId=Q9BTM9-3; Sequence=VSP_054296;
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, ECO:0000269|PubMed:19017811}.
CC -!- SIMILARITY: Belongs to the URM1 family. {ECO:0000255|HAMAP-
CC Rule:MF_03048}.
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DR EMBL; AK001880; BAG50985.1; -; mRNA.
DR EMBL; AK300877; BAG62520.1; -; mRNA.
DR EMBL; AL359091; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471090; EAW87782.1; -; Genomic_DNA.
DR EMBL; BC003581; AAH03581.1; -; mRNA.
DR CCDS; CCDS48035.1; -. [Q9BTM9-2]
DR CCDS; CCDS59148.1; -. [Q9BTM9-3]
DR CCDS; CCDS6900.1; -. [Q9BTM9-1]
DR RefSeq; NP_001129419.1; NM_001135947.2. [Q9BTM9-2]
DR RefSeq; NP_001252511.1; NM_001265582.1. [Q9BTM9-3]
DR RefSeq; NP_112176.1; NM_030914.3. [Q9BTM9-1]
DR AlphaFoldDB; Q9BTM9; -.
DR SMR; Q9BTM9; -.
DR BioGRID; 123542; 30.
DR DIP; DIP-48631N; -.
DR IntAct; Q9BTM9; 27.
DR STRING; 9606.ENSP00000412922; -.
DR iPTMnet; Q9BTM9; -.
DR PhosphoSitePlus; Q9BTM9; -.
DR BioMuta; URM1; -.
DR DMDM; 68565265; -.
DR EPD; Q9BTM9; -.
DR jPOST; Q9BTM9; -.
DR MassIVE; Q9BTM9; -.
DR MaxQB; Q9BTM9; -.
DR PaxDb; Q9BTM9; -.
DR PeptideAtlas; Q9BTM9; -.
DR PRIDE; Q9BTM9; -.
DR ProteomicsDB; 78999; -. [Q9BTM9-1]
DR ProteomicsDB; 79000; -. [Q9BTM9-2]
DR TopDownProteomics; Q9BTM9-1; -. [Q9BTM9-1]
DR Antibodypedia; 17464; 131 antibodies from 27 providers.
DR DNASU; 81605; -.
DR Ensembl; ENST00000372850.5; ENSP00000361941.1; ENSG00000167118.11. [Q9BTM9-3]
DR Ensembl; ENST00000372853.9; ENSP00000361944.4; ENSG00000167118.11. [Q9BTM9-1]
DR Ensembl; ENST00000483206.2; ENSP00000501135.1; ENSG00000167118.11. [Q9BTM9-2]
DR GeneID; 81605; -.
DR KEGG; hsa:81605; -.
DR MANE-Select; ENST00000372853.9; ENSP00000361944.4; NM_030914.4; NP_112176.1.
DR UCSC; uc004buv.3; human. [Q9BTM9-1]
DR CTD; 81605; -.
DR DisGeNET; 81605; -.
DR GeneCards; URM1; -.
DR HGNC; HGNC:28378; URM1.
DR HPA; ENSG00000167118; Low tissue specificity.
DR MIM; 612693; gene.
DR neXtProt; NX_Q9BTM9; -.
DR OpenTargets; ENSG00000167118; -.
DR PharmGKB; PA162408677; -.
DR VEuPathDB; HostDB:ENSG00000167118; -.
DR eggNOG; KOG4146; Eukaryota.
DR GeneTree; ENSGT00390000005101; -.
DR HOGENOM; CLU_148208_0_1_1; -.
DR InParanoid; Q9BTM9; -.
DR OMA; DYELQPN; -.
DR OrthoDB; 1389193at2759; -.
DR PhylomeDB; Q9BTM9; -.
DR TreeFam; TF336363; -.
DR BioCyc; MetaCyc:ENSG00000167118-MON; -.
DR PathwayCommons; Q9BTM9; -.
DR Reactome; R-HSA-6782315; tRNA modification in the nucleus and cytosol.
DR SignaLink; Q9BTM9; -.
DR UniPathway; UPA00988; -.
DR BioGRID-ORCS; 81605; 496 hits in 1092 CRISPR screens.
DR ChiTaRS; URM1; human.
DR GenomeRNAi; 81605; -.
DR Pharos; Q9BTM9; Tbio.
DR PRO; PR:Q9BTM9; -.
DR Proteomes; UP000005640; Chromosome 9.
DR RNAct; Q9BTM9; protein.
DR Bgee; ENSG00000167118; Expressed in endometrium epithelium and 189 other tissues.
DR ExpressionAtlas; Q9BTM9; baseline and differential.
DR Genevisible; Q9BTM9; HS.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
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; IDA:UniProtKB.
DR GO; GO:0032447; P:protein urmylation; IBA:GO_Central.
DR GO; GO:0034227; P:tRNA thio-modification; IMP:UniProtKB.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IMP: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 Alternative splicing; Cytoplasm; Isopeptide bond; Reference proteome;
KW tRNA processing; Ubl conjugation pathway.
FT CHAIN 1..101
FT /note="Ubiquitin-related modifier 1"
FT /id="PRO_0000089714"
FT MOD_RES 101
FT /note="1-thioglycine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03048,
FT ECO:0000269|PubMed:19017811"
FT CROSSLNK 101
FT /note="Glycyl lysine isopeptide (Gly-Lys) (interchain with
FT K-? in acceptor proteins)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03048"
FT VAR_SEQ 64..101
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_054296"
FT VAR_SEQ 79..101
FT /note="LGELDYQLQDQDSVLFISTLHGG -> LVSTLGDIPPPAPALAASVGKRWAS
FT PQAHIEWLGNPPPHSSPTLRLLESPTPGEEGMGSWGHGSTPPS (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_040026"
SQ SEQUENCE 101 AA; 11380 MW; 8DE9B11957866155 CRC64;
MAAPLSVEVE FGGGAELLFD GIKKHRVTLP GQEEPWDIRN LLIWIKKNLL KERPELFIQG
DSVRPGILVL INDADWELLG ELDYQLQDQD SVLFISTLHG G
