URM1_YEAST
ID URM1_YEAST Reviewed; 99 AA.
AC P40554; D6VVS2;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=Ubiquitin-related modifier 1 {ECO:0000255|HAMAP-Rule:MF_03048};
GN Name=URM1 {ECO:0000255|HAMAP-Rule:MF_03048}; OrderedLocusNames=YIL008W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169870;
RA Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D.,
RA Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E.,
RA Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C.,
RA Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V.,
RA Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.";
RL Nature 387:84-87(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [4]
RP FUNCTION, INTERACTION WITH UBA4, AND MUTAGENESIS OF GLY-99.
RX PubMed=10713047; DOI=10.1074/jbc.275.11.7462;
RA Furukawa K., Mizushima N., Noda T., Ohsumi Y.;
RT "A protein conjugation system in yeast with homology to biosynthetic enzyme
RT reaction of prokaryotes.";
RL J. Biol. Chem. 275:7462-7465(2000).
RN [5]
RP FUNCTION AS UBIQUITIN-LIKE, AND INTERACTION WITH AHP1.
RX PubMed=14555475; DOI=10.1128/ec.2.5.930-936.2003;
RA Goehring A.S., Rivers D.M., Sprague G.F. Jr.;
RT "Attachment of the ubiquitin-related protein Urm1p to the antioxidant
RT protein Ahp1p.";
RL Eukaryot. Cell 2:930-936(2003).
RN [6]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=14551258; DOI=10.1091/mbc.e03-02-0079;
RA Goehring A.S., Rivers D.M., Sprague G.F. Jr.;
RT "Urmylation: a ubiquitin-like pathway that functions during invasive growth
RT and budding in yeast.";
RL Mol. Biol. Cell 14:4329-4341(2003).
RN [7]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [8]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [9]
RP THIOCARBOXYLATION AT GLY-99.
RX PubMed=18491921; DOI=10.1021/bi800477u;
RA Schmitz J., Chowdhury M.M., Haenzelmann P., Nimtz M., Lee E.Y.,
RA Schindelin H., Leimkuehler S.;
RT "The sulfurtransferase activity of Uba4 presents a link between ubiquitin-
RT like protein conjugation and activation of sulfur carrier proteins.";
RL Biochemistry 47:6479-6489(2008).
RN [10]
RP FUNCTION IN 2-THIOLATION OF TRNA.
RX PubMed=18664566; DOI=10.1074/jbc.m804043200;
RA Nakai Y., Nakai M., Hayashi H.;
RT "Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related
RT system that resembles bacterial sulfur transfer systems.";
RL J. Biol. Chem. 283:27469-27476(2008).
RN [11]
RP FUNCTION IN 2-THIOLATION OF TRNA.
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 [12]
RP FUNCTION IN 2-THIOLATION OF TRNA.
RX PubMed=18755837; DOI=10.1261/rna.1184108;
RA Huang B., Lu J., Bystroem A.S.;
RT "A genome-wide screen identifies genes required for formation of the wobble
RT nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces
RT cerevisiae.";
RL RNA 14:2183-2194(2008).
RN [13]
RP FUNCTION IN 2-THIOLATION OF TRNA, INTERACTION WITH NCS2 AND NCS6, AND
RP THIOCARBOXYLATION AT GLY-99.
RX PubMed=19145231; DOI=10.1038/nature07643;
RA Leidel S., Pedrioli P.G.A., Bucher T., Brost R., Costanzo M., Schmidt A.,
RA Aebersold R., Boone C., Hofmann K., Peter M.;
RT "Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of
RT eukaryotic transfer RNA.";
RL Nature 458:228-233(2009).
RN [14]
RP FUNCTION IN 2-THIOLATION OF TRNA, INTERACTION WITH NCS2 AND NCS6,
RP THIOCARBOXYLATION AT GLY-99, AND MUTAGENESIS OF 98-GLY-GLY-99.
RX PubMed=19151091; DOI=10.1093/nar/gkn1023;
RA Noma A., Sakaguchi Y., Suzuki T.;
RT "Mechanistic characterization of the sulfur-relay system for eukaryotic 2-
RT thiouridine biogenesis at tRNA wobble positions.";
RL Nucleic Acids Res. 37:1335-1352(2009).
RN [15]
RP FUNCTION, AND CONJUGATION TO AHP1.
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).
RN [16]
RP STRUCTURE BY NMR.
RX PubMed=16864801; DOI=10.1073/pnas.0604876103;
RA Xu J., Zhang J., Wang L., Zhou J., Huang H., Wu J., Zhong Y., Shi Y.;
RT "Solution structure of Urm1 and its implications for the origin of protein
RT modifiers.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:11625-11630(2006).
RN [17]
RP X-RAY CRYSTALLOGRAPHY (1.44 ANGSTROMS), AND HOMODIMERIZATION.
RX PubMed=18260097; DOI=10.1002/prot.21975;
RA Yu J., Zhou C.Z.;
RT "Crystal structure of the dimeric Urm1 from the yeast Saccharomyces
RT cerevisiae.";
RL Proteins 71:1050-1055(2008).
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 UBA4. The sulfur is
CC then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Prior
CC mcm(5) tRNA modification by the elongator complex is required for 2-
CC thiolation. Also acts as a ubiquitin-like protein (UBL) that is
CC covalently conjugated via an isopeptide bond to lysine residues of
CC target proteins such as AHP1. The thiocarboxylated form serves as
CC substrate for conjugation and oxidative stress specifically induces the
CC formation of UBL-protein conjugates. Indirectly involved in regulation
CC of budding and haploid invasive growth. {ECO:0000269|PubMed:10713047,
CC ECO:0000269|PubMed:14551258, ECO:0000269|PubMed:14555475,
CC ECO:0000269|PubMed:18664566, ECO:0000269|PubMed:18755837,
CC ECO:0000269|PubMed:19017811, ECO:0000269|PubMed:19145231,
CC ECO:0000269|PubMed:19151091, ECO:0000269|PubMed:21209336}.
CC -!- PATHWAY: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA
CC biosynthesis. {ECO:0000255|HAMAP-Rule:MF_03048}.
CC -!- SUBUNIT: Homodimer; homodimerization may provide an autoprotection to
CC the highly active C-terminal residue before attacking its substrates.
CC Interacts with NCS2 and NCS6. Forms a conjugate with the target protein
CC AHP1. {ECO:0000255|HAMAP-Rule:MF_03048, ECO:0000269|PubMed:10713047,
CC ECO:0000269|PubMed:14555475, ECO:0000269|PubMed:19145231,
CC ECO:0000269|PubMed:19151091}.
CC -!- INTERACTION:
CC P40554; P53088: NCS6; NbExp=3; IntAct=EBI-24940, EBI-24137;
CC P40554; P38820: UBA4; NbExp=7; IntAct=EBI-24940, EBI-24676;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
CC -!- PTM: C-terminal thiocarboxylation occurs in 2 steps, it is first acyl-
CC adenylated (-COAMP) via the hesA/moeB/thiF part of UBA4, then
CC thiocarboxylated (-COSH) via the rhodanese domain of UBA4.
CC {ECO:0000255|HAMAP-Rule:MF_03048, ECO:0000269|PubMed:18491921,
CC ECO:0000269|PubMed:19145231, ECO:0000269|PubMed:19151091}.
CC -!- MISCELLANEOUS: Present with 1240 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the URM1 family. {ECO:0000255|HAMAP-
CC Rule:MF_03048}.
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DR EMBL; Z38113; CAA86243.1; -; Genomic_DNA.
DR EMBL; AY558295; AAS56621.1; -; Genomic_DNA.
DR EMBL; BK006942; DAA08538.1; -; Genomic_DNA.
DR PIR; S48449; S48449.
DR RefSeq; NP_012258.3; NM_001179358.3.
DR PDB; 2AX5; NMR; -; A=1-99.
DR PDB; 2PKO; X-ray; 1.80 A; A=1-99.
DR PDB; 2QJL; X-ray; 1.44 A; A=1-99.
DR PDBsum; 2AX5; -.
DR PDBsum; 2PKO; -.
DR PDBsum; 2QJL; -.
DR AlphaFoldDB; P40554; -.
DR BMRB; P40554; -.
DR SMR; P40554; -.
DR BioGRID; 34984; 318.
DR DIP; DIP-1894N; -.
DR IntAct; P40554; 3.
DR MINT; P40554; -.
DR STRING; 4932.YIL008W; -.
DR MaxQB; P40554; -.
DR PaxDb; P40554; -.
DR PRIDE; P40554; -.
DR EnsemblFungi; YIL008W_mRNA; YIL008W; YIL008W.
DR GeneID; 854809; -.
DR KEGG; sce:YIL008W; -.
DR SGD; S000001270; URM1.
DR VEuPathDB; FungiDB:YIL008W; -.
DR eggNOG; KOG4146; Eukaryota.
DR GeneTree; ENSGT00390000005101; -.
DR HOGENOM; CLU_148208_0_0_1; -.
DR InParanoid; P40554; -.
DR OMA; DYELQPN; -.
DR BioCyc; YEAST:G3O-31287-MON; -.
DR UniPathway; UPA00988; -.
DR EvolutionaryTrace; P40554; -.
DR PRO; PR:P40554; -.
DR Proteomes; UP000002311; Chromosome IX.
DR RNAct; P40554; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005829; C:cytosol; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:UniProtKB.
DR GO; GO:0031386; F:protein tag; IDA:SGD.
DR GO; GO:0097163; F:sulfur carrier activity; IMP:UniProtKB.
DR GO; GO:0007114; P:cell budding; IGI:SGD.
DR GO; GO:0034599; P:cellular response to oxidative stress; IDA:SGD.
DR GO; GO:0001403; P:invasive growth in response to glucose limitation; IMP:SGD.
DR GO; GO:0032447; P:protein urmylation; IDA:SGD.
DR GO; GO:0034227; P:tRNA thio-modification; IMP:UniProtKB.
DR GO; GO:0002143; P:tRNA wobble position uridine thiolation; IMP:SGD.
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 3D-structure; Cytoplasm; Isopeptide bond; Nucleus; Reference proteome;
KW tRNA processing; Ubl conjugation pathway.
FT CHAIN 1..99
FT /note="Ubiquitin-related modifier 1"
FT /id="PRO_0000203002"
FT MOD_RES 99
FT /note="1-thioglycine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03048,
FT ECO:0000269|PubMed:18491921, ECO:0000269|PubMed:19145231,
FT ECO:0000269|PubMed:19151091"
FT CROSSLNK 99
FT /note="Glycyl lysine isopeptide (Gly-Lys) (interchain with
FT K-? in acceptor proteins)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03048"
FT MUTAGEN 98..99
FT /note="Missing: Abolishes thiocarboxylation and function in
FT 2-Thiolation of tRNA."
FT /evidence="ECO:0000269|PubMed:19151091"
FT MUTAGEN 99
FT /note="Missing: Abolishes URM1 conjugate formation."
FT /evidence="ECO:0000269|PubMed:10713047"
FT STRAND 2..9
FT /evidence="ECO:0007829|PDB:2QJL"
FT HELIX 12..15
FT /evidence="ECO:0007829|PDB:2QJL"
FT TURN 16..18
FT /evidence="ECO:0007829|PDB:2QJL"
FT STRAND 21..26
FT /evidence="ECO:0007829|PDB:2QJL"
FT HELIX 34..44
FT /evidence="ECO:0007829|PDB:2QJL"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:2QJL"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:2QJL"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:2PKO"
FT STRAND 65..69
FT /evidence="ECO:0007829|PDB:2QJL"
FT HELIX 74..77
FT /evidence="ECO:0007829|PDB:2QJL"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:2QJL"
FT STRAND 89..94
FT /evidence="ECO:0007829|PDB:2QJL"
SQ SEQUENCE 99 AA; 11028 MW; A15356D6C1B6B5BC CRC64;
MVNVKVEFLG GLDAIFGKQR VHKIKMDKED PVTVGDLIDH IVSTMINNPN DVSIFIEDDS
IRPGIITLIN DTDWELEGEK DYILEDGDII SFTSTLHGG
