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Protein

Ubiquitin-related modifier 1

Gene

URM1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts as a sulfur carrier required for 2-thiolation of mcm5S2U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln). Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by MOCS3. The sulfur is then transferred to tRNA to form 2-thiolation of mcm5S2U. Also acts as a ubiquitin-like protein (UBL) that is covalently conjugated via an isopeptide bond to lysine residues of target proteins such as MOCS3, ATPBD3, CTU2, USP15 and CAS. The thiocarboxylated form serves as substrate for conjugation and oxidative stress specifically induces the formation of UBL-protein conjugates.UniRule annotation2 Publications

Pathwayi: 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis

This protein is involved in the pathway 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis, which is part of tRNA modification.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis and in tRNA modification.

GO - Biological processi

  • gene expression Source: Reactome
  • protein urmylation Source: UniProtKB-HAMAP
  • tRNA modification Source: Reactome
  • tRNA processing Source: Reactome
  • tRNA thio-modification Source: UniProtKB
  • tRNA wobble uridine modification Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

tRNA processing, Ubl conjugation pathway

Enzyme and pathway databases

ReactomeiR-HSA-6782315. tRNA modification in the nucleus and cytosol.
UniPathwayiUPA00988.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-related modifier 1UniRule annotation
Gene namesi
Name:URM1UniRule annotation
Synonyms:C9orf74
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

HGNCiHGNC:28378. URM1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • extracellular exosome Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA162408677.

Polymorphism and mutation databases

BioMutaiURM1.
DMDMi68565265.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 101101Ubiquitin-related modifier 1PRO_0000089714Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei101 – 10111-thioglycineUniRule annotation1 Publication
Cross-linki101 – 101Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)UniRule annotation

Post-translational modificationi

C-terminal thiocarboxylation occurs in 2 steps, it is first acyl-adenylated (-COAMP) via the hesA/moeB/thiF part of MOCS3, then thiocarboxylated (-COSH) via the rhodanese domain of MOCS3.UniRule annotation1 Publication

Keywords - PTMi

Isopeptide bond

Proteomic databases

EPDiQ9BTM9.
MaxQBiQ9BTM9.
PaxDbiQ9BTM9.
PRIDEiQ9BTM9.
TopDownProteomicsiQ9BTM9-1. [Q9BTM9-1]

Expressioni

Gene expression databases

BgeeiQ9BTM9.
CleanExiHS_URM1.
ExpressionAtlasiQ9BTM9. baseline and differential.
GenevisibleiQ9BTM9. HS.

Organism-specific databases

HPAiHPA053645.
HPA065160.

Interactioni

Subunit structurei

Component of a complex at least composed of URM1, CTU2/NCS2 and CTU1/ATPBD3.UniRule annotation1 Publication

Protein-protein interaction databases

BioGridi123542. 16 interactions.
DIPiDIP-48631N.
IntActiQ9BTM9. 5 interactions.
MINTiMINT-1401016.
STRINGi9606.ENSP00000412922.

Structurei

3D structure databases

ProteinModelPortaliQ9BTM9.
SMRiQ9BTM9. Positions 1-101.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the URM1 family.UniRule annotation

Phylogenomic databases

eggNOGiKOG4146. Eukaryota.
COG5131. LUCA.
GeneTreeiENSGT00390000005101.
HOGENOMiHOG000280990.
HOVERGENiHBG059837.
InParanoidiQ9BTM9.
KOiK12161.
OMAiDSILFIS.
OrthoDBiEOG7DRJ5B.
PhylomeDBiQ9BTM9.
TreeFamiTF336363.

Family and domain databases

Gene3Di3.10.20.30. 1 hit.
HAMAPiMF_03048. Urm1.
InterProiIPR012675. Beta-grasp_dom.
IPR016155. Mopterin_synth/thiamin_S_b.
IPR015221. Urm1.
[Graphical view]
PANTHERiPTHR14986:SF4. PTHR14986:SF4. 1 hit.
PfamiPF09138. Urm1. 1 hit.
[Graphical view]
PIRSFiPIRSF037379. Ubiquitin-related_modifier_1. 1 hit.
SUPFAMiSSF54285. SSF54285. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BTM9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAAPLSVEVE FGGGAELLFD GIKKHRVTLP GQEEPWDIRN LLIWIKKNLL
60 70 80 90 100
KERPELFIQG DSVRPGILVL INDADWELLG ELDYQLQDQD SVLFISTLHG

G
Length:101
Mass (Da):11,380
Last modified:June 1, 2001 - v1
Checksum:i8DE9B11957866155
GO
Isoform 2 (identifier: Q9BTM9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     79-101: LGELDYQLQDQDSVLFISTLHGG → LVSTLGDIPP...SWGHGSTPPS

Show »
Length:146
Mass (Da):15,815
Checksum:iC52CEFA6A2E72779
GO
Isoform 3 (identifier: Q9BTM9-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     64-101: Missing.

Note: No experimental confirmation available. Gene prediction based on EST data.
Show »
Length:63
Mass (Da):7,143
Checksum:i96BA93664527546A
GO

Sequence cautioni

The sequence CAI13492.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei64 – 10138Missing in isoform 3. CuratedVSP_054296Add
BLAST
Alternative sequencei79 – 10123LGELD…TLHGG → LVSTLGDIPPPAPALAASVG KRWASPQAHIEWLGNPPPHS SPTLRLLESPTPGEEGMGSW GHGSTPPS in isoform 2. 1 PublicationVSP_040026Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001880 mRNA. Translation: BAG50985.1.
AK300877 mRNA. Translation: BAG62520.1.
AL359091 Genomic DNA. Translation: CAI13492.1. Sequence problems.
AL359091 Genomic DNA. Translation: CAI13493.1.
CH471090 Genomic DNA. Translation: EAW87782.1.
BC003581 mRNA. Translation: AAH03581.1.
CCDSiCCDS48035.1. [Q9BTM9-2]
CCDS59148.1. [Q9BTM9-3]
CCDS6900.1. [Q9BTM9-1]
RefSeqiNP_001129419.1. NM_001135947.2. [Q9BTM9-2]
NP_001252511.1. NM_001265582.1. [Q9BTM9-3]
NP_112176.1. NM_030914.3. [Q9BTM9-1]
UniGeneiHs.495229.

Genome annotation databases

EnsembliENST00000372850; ENSP00000361941; ENSG00000167118. [Q9BTM9-3]
ENST00000372853; ENSP00000361944; ENSG00000167118. [Q9BTM9-1]
ENST00000452446; ENSP00000412922; ENSG00000167118. [Q9BTM9-2]
GeneIDi81605.
KEGGihsa:81605.
UCSCiuc004buv.3. human. [Q9BTM9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK001880 mRNA. Translation: BAG50985.1.
AK300877 mRNA. Translation: BAG62520.1.
AL359091 Genomic DNA. Translation: CAI13492.1. Sequence problems.
AL359091 Genomic DNA. Translation: CAI13493.1.
CH471090 Genomic DNA. Translation: EAW87782.1.
BC003581 mRNA. Translation: AAH03581.1.
CCDSiCCDS48035.1. [Q9BTM9-2]
CCDS59148.1. [Q9BTM9-3]
CCDS6900.1. [Q9BTM9-1]
RefSeqiNP_001129419.1. NM_001135947.2. [Q9BTM9-2]
NP_001252511.1. NM_001265582.1. [Q9BTM9-3]
NP_112176.1. NM_030914.3. [Q9BTM9-1]
UniGeneiHs.495229.

3D structure databases

ProteinModelPortaliQ9BTM9.
SMRiQ9BTM9. Positions 1-101.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123542. 16 interactions.
DIPiDIP-48631N.
IntActiQ9BTM9. 5 interactions.
MINTiMINT-1401016.
STRINGi9606.ENSP00000412922.

Polymorphism and mutation databases

BioMutaiURM1.
DMDMi68565265.

Proteomic databases

EPDiQ9BTM9.
MaxQBiQ9BTM9.
PaxDbiQ9BTM9.
PRIDEiQ9BTM9.
TopDownProteomicsiQ9BTM9-1. [Q9BTM9-1]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000372850; ENSP00000361941; ENSG00000167118. [Q9BTM9-3]
ENST00000372853; ENSP00000361944; ENSG00000167118. [Q9BTM9-1]
ENST00000452446; ENSP00000412922; ENSG00000167118. [Q9BTM9-2]
GeneIDi81605.
KEGGihsa:81605.
UCSCiuc004buv.3. human. [Q9BTM9-1]

Organism-specific databases

CTDi81605.
GeneCardsiURM1.
HGNCiHGNC:28378. URM1.
HPAiHPA053645.
HPA065160.
MIMi612693. gene.
neXtProtiNX_Q9BTM9.
PharmGKBiPA162408677.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4146. Eukaryota.
COG5131. LUCA.
GeneTreeiENSGT00390000005101.
HOGENOMiHOG000280990.
HOVERGENiHBG059837.
InParanoidiQ9BTM9.
KOiK12161.
OMAiDSILFIS.
OrthoDBiEOG7DRJ5B.
PhylomeDBiQ9BTM9.
TreeFamiTF336363.

Enzyme and pathway databases

UniPathwayiUPA00988.
ReactomeiR-HSA-6782315. tRNA modification in the nucleus and cytosol.

Miscellaneous databases

ChiTaRSiURM1. human.
GenomeRNAii81605.
NextBioi71912.
PROiQ9BTM9.
SOURCEiSearch...

Gene expression databases

BgeeiQ9BTM9.
CleanExiHS_URM1.
ExpressionAtlasiQ9BTM9. baseline and differential.
GenevisibleiQ9BTM9. HS.

Family and domain databases

Gene3Di3.10.20.30. 1 hit.
HAMAPiMF_03048. Urm1.
InterProiIPR012675. Beta-grasp_dom.
IPR016155. Mopterin_synth/thiamin_S_b.
IPR015221. Urm1.
[Graphical view]
PANTHERiPTHR14986:SF4. PTHR14986:SF4. 1 hit.
PfamiPF09138. Urm1. 1 hit.
[Graphical view]
PIRSFiPIRSF037379. Ubiquitin-related_modifier_1. 1 hit.
SUPFAMiSSF54285. SSF54285. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Tissue: Placenta and Small intestine.
  2. "DNA sequence and analysis of human chromosome 9."
    Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L.
    , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I.
    Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Placenta.
  5. "A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway."
    Schlieker C.D., Van der Veen A.G., Damon J.R., Spooner E., Ploegh H.L.
    Proc. Natl. Acad. Sci. U.S.A. 105:18255-18260(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN 2-THIOLATION OF TRNA, IDENTIFICATION IN A COMPLEX WITH CTU1 AND C16ORF84, THIOCARBOXYLATION AT GLY-101.
  6. "Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed protein modifier."
    Van der Veen A.G., Schorpp K., Schlieker C., Buti L., Damon J.R., Spooner E., Ploegh H.L., Jentsch S.
    Proc. Natl. Acad. Sci. U.S.A. 108:1763-1770(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROTEIN CONJUGATION, IDENTIFICATION OF SUBSTRATES.

Entry informationi

Entry nameiURM1_HUMAN
AccessioniPrimary (citable) accession number: Q9BTM9
Secondary accession number(s): B3KMH3, B4DV08, Q5T4B4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: June 1, 2001
Last modified: March 16, 2016
This is version 118 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.