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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)DescriptionActionsGraphical viewLength
Mutagenesisi98 – 99Missing : Abolishes thiocarboxylation and function in 2-Thiolation of tRNA. 1 Publication2
Mutagenesisi99Missing : Abolishes URM1 conjugate formation. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002030021 – 99Ubiquitin-related modifier 1Add BLAST99

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei991-thioglycineUniRule annotation3 Publications1
Cross-linki99Glycyl 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.
PRIDEiP40554.

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. 127 interactors.
DIPiDIP-1894N.
IntActiP40554. 1 interactor.
MINTiMINT-395676.

Structurei

Secondary structure

199
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 9Combined sources8
Helixi12 – 15Combined sources4
Turni16 – 18Combined sources3
Beta strandi21 – 26Combined sources6
Helixi34 – 44Combined sources11
Helixi49 – 51Combined sources3
Helixi52 – 55Combined sources4
Beta strandi56 – 61Combined sources6
Beta strandi65 – 69Combined sources5
Helixi74 – 77Combined sources4
Helixi79 – 81Combined sources3
Beta strandi89 – 94Combined sources6

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP40554.

Family & Domainsi

Sequence similaritiesi

Belongs to the URM1 family.UniRule annotation

Phylogenomic databases

GeneTreeiENSGT00390000005101.
HOGENOMiHOG000280990.
InParanoidiP40554.
KOiK12161.
OMAiDWELEGM.
OrthoDBiEOG092C5T2V.

Family and domain databases

CDDicd01764. Urm1. 1 hit.
Gene3Di3.10.20.30. 1 hit.
HAMAPiMF_03048. Urm1. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2AX5NMR-A1-99[»]
2PKOX-ray1.80A1-99[»]
2QJLX-ray1.44A1-99[»]
ProteinModelPortaliP40554.
SMRiP40554.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34984. 127 interactors.
DIPiDIP-1894N.
IntActiP40554. 1 interactor.
MINTiMINT-395676.

Proteomic databases

MaxQBiP40554.
PRIDEiP40554.

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.
OMAiDWELEGM.
OrthoDBiEOG092C5T2V.

Enzyme and pathway databases

UniPathwayiUPA00988.
BioCyciYEAST:G3O-31287-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP40554.
PROiP40554.

Family and domain databases

CDDicd01764. Urm1. 1 hit.
Gene3Di3.10.20.30. 1 hit.
HAMAPiMF_03048. Urm1. 1 hit.
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...

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: November 2, 2016
This is version 138 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.