ID   URM1_ORYSJ              Reviewed;         100 AA.
AC   Q0D6M1; Q7EYM5; Q8S938;
DT   24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT   17-OCT-2006, sequence version 1.
DT   03-AUG-2022, entry version 86.
DE   RecName: Full=Ubiquitin-related modifier 1 homolog {ECO:0000255|HAMAP-Rule:MF_03048};
GN   Name=URM1 {ECO:0000255|HAMAP-Rule:MF_03048};
GN   OrderedLocusNames=Os07g0466300, LOC_Os07g28280;
GN   ORFNames=OsJ_023216, P0404G11.126-1;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=cv. Gimbozu;
RX   PubMed=12520304; DOI=10.1038/nature01219;
RA   Nakazaki T., Okumoto Y., Horibata A., Yamahira S., Teraishi M., Nishida H.,
RA   Inoue H., Tanisaka T.;
RT   "Mobilization of a transposon in the rice genome.";
RL   Nature 421:170-172(2003).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(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. The
CC       thiocarboxylated form serves as substrate for conjugation and oxidative
CC       stress specifically induces the formation of UBL-protein conjugates.
CC       {ECO:0000255|HAMAP-Rule:MF_03048}.
CC   -!- PATHWAY: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA
CC       biosynthesis. {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 the MOCS3 homolog,
CC       then thiocarboxylated (-COSH) via the rhodanese domain of the MOCS3
CC       homolog. {ECO:0000255|HAMAP-Rule:MF_03048}.
CC   -!- SIMILARITY: Belongs to the URM1 family. {ECO:0000255|HAMAP-
CC       Rule:MF_03048}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAC84286.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AB072933; BAB88939.1; -; Genomic_DNA.
DR   EMBL; AP005448; BAC84286.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008213; BAF21502.1; -; Genomic_DNA.
DR   EMBL; AP014963; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CM000144; EAZ39733.1; -; Genomic_DNA.
DR   RefSeq; XP_015645398.1; XM_015789912.1.
DR   AlphaFoldDB; Q0D6M1; -.
DR   SMR; Q0D6M1; -.
DR   STRING; 4530.OS07T0466300-01; -.
DR   PaxDb; Q0D6M1; -.
DR   PRIDE; Q0D6M1; -.
DR   GeneID; 4343175; -.
DR   KEGG; osa:4343175; -.
DR   InParanoid; Q0D6M1; -.
DR   OrthoDB; 1541629at2759; -.
DR   UniPathway; UPA00988; -.
DR   Proteomes; UP000000763; Chromosome 7.
DR   Proteomes; UP000007752; Chromosome 7.
DR   Proteomes; UP000059680; Chromosome 7.
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:0032447; P:protein urmylation; IBA:GO_Central.
DR   GO; GO:0034227; P:tRNA thio-modification; IEA:UniProtKB-UniRule.
DR   GO; GO:0002098; P:tRNA wobble uridine modification; IEA:UniProtKB-UniRule.
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   3: Inferred from homology;
KW   Cytoplasm; Isopeptide bond; Reference proteome; tRNA processing;
KW   Ubl conjugation pathway.
FT   CHAIN           1..100
FT                   /note="Ubiquitin-related modifier 1 homolog"
FT                   /id="PRO_0000367870"
FT   MOD_RES         100
FT                   /note="1-thioglycine"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03048"
FT   CROSSLNK        100
FT                   /note="Glycyl lysine isopeptide (Gly-Lys) (interchain with
FT                   K-? in acceptor proteins)"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03048"
SQ   SEQUENCE   100 AA;  10986 MW;  9C58CFED83865963 CRC64;
     MHLTLEFGGG LELLLEKSTK VHKVDLQPND GDGKVVMKGL LAWVKSNLIK ERPEMFLKGD
     SVRPGVLVLI NDCDWELCGG LDAELEEKDV VVFISTLHGG