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Protein

Ubiquitin-related modifier 1

Gene

URM1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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 UBA4. The sulfur is then transferred to tRNA to form 2-thiolation of mcm5S2U. Prior mcm5 tRNA modification by the elongator complex is required for 2-thiolation. Also acts as a ubiquitin-like protein (UBL) that is covalently conjugated via an isopeptide bond to lysine residues of target proteins such as AHP1. The thiocarboxylated form serves as substrate for conjugation and oxidative stress specifically induces the formation of UBL-protein conjugates. Indirectly involved in regulation of budding and haploid invasive growth.9 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 - Molecular functioni

  • protein homodimerization activity Source: UniProtKB
  • protein tag Source: SGD

GO - Biological processi

  • cell budding Source: SGD
  • cellular response to oxidative stress Source: SGD
  • invasive growth in response to glucose limitation Source: SGD
  • protein urmylation Source: SGD
  • tRNA thio-modification Source: UniProtKB
  • tRNA wobble position uridine thiolation Source: SGD
  • tRNA wobble uridine modification Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

tRNA processing, Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-31287-MONOMER.
UniPathwayiUPA00988.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-related modifier 1UniRule annotation
Gene namesi
Name:URM1UniRule annotation
Ordered Locus Names:YIL008W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IX

Organism-specific databases

EuPathDBiFungiDB:YIL008W.
SGDiS000001270. URM1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytosol Source: UniProtKB
  • nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi98 – 992Missing : Abolishes thiocarboxylation and function in 2-Thiolation of tRNA. 1 Publication
Mutagenesisi99 – 991Missing : Abolishes URM1 conjugate formation. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9999Ubiquitin-related modifier 1PRO_0000203002Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei99 – 9911-thioglycineUniRule annotation3 Publications
Cross-linki99 – 99Glycyl 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 UBA4, then thiocarboxylated (-COSH) via the rhodanese domain of UBA4.UniRule annotation3 Publications

Keywords - PTMi

Isopeptide bond

Proteomic databases

MaxQBiP40554.
PeptideAtlasiP40554.

Interactioni

Subunit structurei

Homodimer; homodimerization may provide an autoprotection to the highly active C-terminal residue before attacking its substrates. Interacts with NCS2 and NCS6. Forms a conjugate with the target protein AHP1.UniRule annotation4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
UBA4P388204EBI-24940,EBI-24676

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi34984. 126 interactions.
DIPiDIP-1894N.
IntActiP40554. 1 interaction.
MINTiMINT-395676.

Structurei

Secondary structure

1
99
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 98Combined sources
Helixi12 – 154Combined sources
Turni16 – 183Combined sources
Beta strandi21 – 266Combined sources
Helixi34 – 4411Combined sources
Helixi49 – 513Combined sources
Helixi52 – 554Combined sources
Beta strandi56 – 616Combined sources
Beta strandi65 – 695Combined sources
Helixi74 – 774Combined sources
Helixi79 – 813Combined sources
Beta strandi89 – 946Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AX5NMR-A1-99[»]
2PKOX-ray1.80A1-99[»]
2QJLX-ray1.44A1-99[»]
ProteinModelPortaliP40554.
SMRiP40554. Positions 1-99.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP40554.

Family & Domainsi

Sequence similaritiesi

Belongs to the URM1 family.UniRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000005101.
HOGENOMiHOG000280990.
InParanoidiP40554.
KOiK12161.
OMAiMMGTPEL.
OrthoDBiEOG7W15H8.

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.

P40554-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVNVKVEFLG GLDAIFGKQR VHKIKMDKED PVTVGDLIDH IVSTMINNPN
60 70 80 90
DVSIFIEDDS IRPGIITLIN DTDWELEGEK DYILEDGDII SFTSTLHGG
Length:99
Mass (Da):11,028
Last modified:February 1, 1995 - v1
Checksum:iA15356D6C1B6B5BC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38113 Genomic DNA. Translation: CAA86243.1.
AY558295 Genomic DNA. Translation: AAS56621.1.
BK006942 Genomic DNA. Translation: DAA08538.1.
PIRiS48449.
RefSeqiNP_012258.3. NM_001179358.3.

Genome annotation databases

EnsemblFungiiYIL008W; YIL008W; YIL008W.
GeneIDi854809.
KEGGisce:YIL008W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38113 Genomic DNA. Translation: CAA86243.1.
AY558295 Genomic DNA. Translation: AAS56621.1.
BK006942 Genomic DNA. Translation: DAA08538.1.
PIRiS48449.
RefSeqiNP_012258.3. NM_001179358.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2AX5NMR-A1-99[»]
2PKOX-ray1.80A1-99[»]
2QJLX-ray1.44A1-99[»]
ProteinModelPortaliP40554.
SMRiP40554. Positions 1-99.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34984. 126 interactions.
DIPiDIP-1894N.
IntActiP40554. 1 interaction.
MINTiMINT-395676.

Proteomic databases

MaxQBiP40554.
PeptideAtlasiP40554.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYIL008W; YIL008W; YIL008W.
GeneIDi854809.
KEGGisce:YIL008W.

Organism-specific databases

EuPathDBiFungiDB:YIL008W.
SGDiS000001270. URM1.

Phylogenomic databases

GeneTreeiENSGT00390000005101.
HOGENOMiHOG000280990.
InParanoidiP40554.
KOiK12161.
OMAiMMGTPEL.
OrthoDBiEOG7W15H8.

Enzyme and pathway databases

UniPathwayiUPA00988.
BioCyciYEAST:G3O-31287-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP40554.
PROiP40554.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. "A protein conjugation system in yeast with homology to biosynthetic enzyme reaction of prokaryotes."
    Furukawa K., Mizushima N., Noda T., Ohsumi Y.
    J. Biol. Chem. 275:7462-7465(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH UBA4, MUTAGENESIS OF GLY-99.
  5. "Attachment of the ubiquitin-related protein Urm1p to the antioxidant protein Ahp1p."
    Goehring A.S., Rivers D.M., Sprague G.F. Jr.
    Eukaryot. Cell 2:930-936(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS UBIQUITIN-LIKE, INTERACTION WITH AHP1.
  6. "Urmylation: a ubiquitin-like pathway that functions during invasive growth and budding in yeast."
    Goehring A.S., Rivers D.M., Sprague G.F. Jr.
    Mol. Biol. Cell 14:4329-4341(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  7. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  9. "The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins."
    Schmitz J., Chowdhury M.M., Haenzelmann P., Nimtz M., Lee E.Y., Schindelin H., Leimkuehler S.
    Biochemistry 47:6479-6489(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: THIOCARBOXYLATION AT GLY-99.
  10. "Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems."
    Nakai Y., Nakai M., Hayashi H.
    J. Biol. Chem. 283:27469-27476(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN 2-THIOLATION OF TRNA.
  11. "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.
  12. "A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae."
    Huang B., Lu J., Bystroem A.S.
    RNA 14:2183-2194(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN 2-THIOLATION OF TRNA.
  13. "Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA."
    Leidel S., Pedrioli P.G.A., Bucher T., Brost R., Costanzo M., Schmidt A., Aebersold R., Boone C., Hofmann K., Peter M.
    Nature 458:228-233(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN 2-THIOLATION OF TRNA, INTERACTION WITH NCS2 AND NCS6, THIOCARBOXYLATION AT GLY-99.
  14. "Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions."
    Noma A., Sakaguchi Y., Suzuki T.
    Nucleic Acids Res. 37:1335-1352(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN 2-THIOLATION OF TRNA, INTERACTION WITH NCS2 AND NCS6, THIOCARBOXYLATION AT GLY-99, MUTAGENESIS OF 98-GLY-GLY-99.
  15. "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, CONJUGATION TO AHP1.
  16. "Solution structure of Urm1 and its implications for the origin of protein modifiers."
    Xu J., Zhang J., Wang L., Zhou J., Huang H., Wu J., Zhong Y., Shi Y.
    Proc. Natl. Acad. Sci. U.S.A. 103:11625-11630(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.
  17. "Crystal structure of the dimeric Urm1 from the yeast Saccharomyces cerevisiae."
    Yu J., Zhou C.Z.
    Proteins 71:1050-1055(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.44 ANGSTROMS), HOMODIMERIZATION.

Entry informationi

Entry nameiURM1_YEAST
AccessioniPrimary (citable) accession number: P40554
Secondary accession number(s): D6VVS2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: June 8, 2016
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1240 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome IX
    Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

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.