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Protein

Ubiquitin-related modifier 1

Gene

Urm1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 3 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 annotation

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 - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

tRNA processing, Ubl conjugation pathway

Enzyme and pathway databases

UniPathwayiUPA00988.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-related modifier 1UniRule annotation
Gene namesi
Name:Urm1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:1915455. Urm1.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 101101Ubiquitin-related modifier 1PRO_0000089715Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Isopeptide bond

Proteomic databases

MaxQBiQ9D2P4.
PaxDbiQ9D2P4.
PeptideAtlasiQ9D2P4.
PRIDEiQ9D2P4.

PTM databases

iPTMnetiQ9D2P4.

Expressioni

Gene expression databases

BgeeiQ9D2P4.
GenevisibleiQ9D2P4. MM.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000088676.

Structurei

Secondary structure

1
101
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 117Combined sources
Turni13 – 153Combined sources
Helixi16 – 183Combined sources
Turni19 – 213Combined sources
Beta strandi23 – 297Combined sources
Beta strandi31 – 333Combined sources
Helixi38 – 458Combined sources
Turni46 – 494Combined sources
Helixi54 – 574Combined sources
Beta strandi60 – 623Combined sources
Beta strandi65 – 7511Combined sources
Helixi76 – 794Combined sources
Turni81 – 833Combined sources
Beta strandi88 – 969Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WGKNMR-A1-101[»]
1XO3NMR-A2-101[»]
ProteinModelPortaliQ9D2P4.
SMRiQ9D2P4. Positions 1-101.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9D2P4.

Family & Domainsi

Sequence similaritiesi

Belongs to the URM1 family.UniRule annotation

Phylogenomic databases

eggNOGiKOG4146. Eukaryota.
COG5131. LUCA.
GeneTreeiENSGT00390000005101.
HOGENOMiHOG000280990.
HOVERGENiHBG059837.
InParanoidiQ9D2P4.
KOiK12161.
OMAiDSILFIS.
OrthoDBiEOG7DRJ5B.
PhylomeDBiQ9D2P4.
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.

Sequencei

Sequence statusi: Complete.

Q9D2P4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAPLCVKVE FGGGAELLFD GVKKHQVALP GQEEPWDIRN LLVWIKKNLL
60 70 80 90 100
KERPELFIQG DSVRPGILVL INDADWELLG ELDYQLQDQD SILFISTLHG

G
Length:101
Mass (Da):11,323
Last modified:June 1, 2001 - v1
Checksum:i535D437F0D32929E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti31 – 311G → R in BAC33621 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK019352 mRNA. Translation: BAB31673.1.
AK049227 mRNA. Translation: BAC33621.1.
AK049849 mRNA. Translation: BAC33956.1.
AL928926 Genomic DNA. Translation: CAM46216.1.
CH466542 Genomic DNA. Translation: EDL08423.1.
BC026994 mRNA. Translation: AAH26994.1.
CCDSiCCDS15859.1.
RefSeqiNP_080891.1. NM_026615.4.
UniGeneiMm.20273.

Genome annotation databases

EnsembliENSMUST00000091142; ENSMUSP00000088676; ENSMUSG00000069020.
GeneIDi68205.
KEGGimmu:68205.
UCSCiuc008jag.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK019352 mRNA. Translation: BAB31673.1.
AK049227 mRNA. Translation: BAC33621.1.
AK049849 mRNA. Translation: BAC33956.1.
AL928926 Genomic DNA. Translation: CAM46216.1.
CH466542 Genomic DNA. Translation: EDL08423.1.
BC026994 mRNA. Translation: AAH26994.1.
CCDSiCCDS15859.1.
RefSeqiNP_080891.1. NM_026615.4.
UniGeneiMm.20273.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WGKNMR-A1-101[»]
1XO3NMR-A2-101[»]
ProteinModelPortaliQ9D2P4.
SMRiQ9D2P4. Positions 1-101.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000088676.

PTM databases

iPTMnetiQ9D2P4.

Proteomic databases

MaxQBiQ9D2P4.
PaxDbiQ9D2P4.
PeptideAtlasiQ9D2P4.
PRIDEiQ9D2P4.

Protocols and materials databases

DNASUi68205.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000091142; ENSMUSP00000088676; ENSMUSG00000069020.
GeneIDi68205.
KEGGimmu:68205.
UCSCiuc008jag.1. mouse.

Organism-specific databases

CTDi81605.
MGIiMGI:1915455. Urm1.

Phylogenomic databases

eggNOGiKOG4146. Eukaryota.
COG5131. LUCA.
GeneTreeiENSGT00390000005101.
HOGENOMiHOG000280990.
HOVERGENiHBG059837.
InParanoidiQ9D2P4.
KOiK12161.
OMAiDSILFIS.
OrthoDBiEOG7DRJ5B.
PhylomeDBiQ9D2P4.
TreeFamiTF336363.

Enzyme and pathway databases

UniPathwayiUPA00988.

Miscellaneous databases

ChiTaRSiUrm1. mouse.
EvolutionaryTraceiQ9D2P4.
PROiQ9D2P4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9D2P4.
GenevisibleiQ9D2P4. MM.

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. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Hippocampus.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    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].
    Tissue: Eye.
  5. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain and Testis.
  6. "Solution structure of mouse hypothetical protein 2900073H19RIK."
    RIKEN structural genomics initiative (RSGI)
    Submitted (MAY-2004) to the PDB data bank
    Cited for: STRUCTURE BY NMR.
  7. "Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1."
    Singh S., Tonelli M., Tyler R.C., Bahrami A., Lee M.S., Markley J.L.
    Protein Sci. 14:2095-2102(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 2-101.

Entry informationi

Entry nameiURM1_MOUSE
AccessioniPrimary (citable) accession number: Q9D2P4
Secondary accession number(s): A3KGW2, Q8BHY9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: June 1, 2001
Last modified: July 6, 2016
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.