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Protein

NEDD8-conjugating enzyme UBC12

Gene

UBC12

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

Accepts the ubiquitin-like protein NEDD8/RUB1 from the UBA3-ULA1 E1 complex and catalyzes its covalent attachment to other proteins. The major substrate is CDC53/Cullin.1 Publication

Catalytic activityi

ATP + NEDD8 + protein lysine = AMP + diphosphate + protein N-NEDD8yllysine.

Pathwayi: protein neddylation

This protein is involved in the pathway protein neddylation, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway protein neddylation and in Protein modification.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei115Glycyl thioester intermediatePROSITE-ProRule annotation1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ligase activity Source: UniProtKB-KW
  • NEDD8 transferase activity Source: SGD

GO - Biological processi

  • protein neddylation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-32394-MONOMER.
UniPathwayiUPA00885.

Names & Taxonomyi

Protein namesi
Recommended name:
NEDD8-conjugating enzyme UBC12 (EC:6.3.2.-)
Alternative name(s):
RUB1-conjugating enzyme
RUB1-protein ligase
Ubiquitin carrier protein 12
Gene namesi
Name:UBC12
Ordered Locus Names:YLR306W
ORF Names:L2142.3
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR306W.
SGDiS000004297. UBC12.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000825011 – 188NEDD8-conjugating enzyme UBC12Add BLAST188

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionine1 Publication1

Post-translational modificationi

The acetylation of Met-1 is cotranslational, and not regulatory. The N-acetylmethionine increases affinity for DCUN1D1 by about 2 orders of magnitude and is crucial for NEDD8 transfer to cullins.1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP52491.
PRIDEiP52491.

Interactioni

Subunit structurei

Interacts with DCN1.1 Publication

Protein-protein interaction databases

BioGridi31571. 32 interactors.
DIPiDIP-2051N.
IntActiP52491. 1 interactor.
MINTiMINT-552826.

Structurei

Secondary structure

1188
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi1 – 19Combined sources19
Beta strandi20 – 22Combined sources3
Helixi27 – 37Combined sources11
Beta strandi45 – 51Combined sources7
Beta strandi63 – 68Combined sources6
Beta strandi71 – 73Combined sources3
Turni74 – 77Combined sources4
Beta strandi80 – 85Combined sources6
Turni88 – 92Combined sources5
Beta strandi96 – 99Combined sources4
Beta strandi112 – 114Combined sources3
Helixi117 – 119Combined sources3
Turni120 – 122Combined sources3
Helixi129 – 141Combined sources13
Helixi151 – 158Combined sources8
Helixi161 – 172Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3O2UX-ray2.00A/B1-188[»]
3TDIX-ray2.30C/D1-24[»]
ProteinModelPortaliP52491.
SMRiP52491.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP52491.

Family & Domainsi

Sequence similaritiesi

Belongs to the ubiquitin-conjugating enzyme family. UBC12 subfamily.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00630000089859.
HOGENOMiHOG000233456.
InParanoidiP52491.
KOiK10579.
OMAiYHPNIDI.
OrthoDBiEOG092C5L1U.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P52491-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKLRQLQKK KQKENENSSS IQPNLSAARI RLKRDLDSLD LPPTVTLNVI
60 70 80 90 100
TSPDSADRSQ SPKLEVIVRP DEGYYNYGSI NFNLDFNEVY PIEPPKVVCL
110 120 130 140 150
KKIFHPNIDL KGNVCLNILR EDWSPALDLQ SIITGLLFLF LEPNPNDPLN
160 170 180
KDAAKLLCEG EKEFAEAVRL TMSGGSIEHV KYDNIVSP
Length:188
Mass (Da):21,203
Last modified:October 1, 1996 - v1
Checksum:iBEEECF40B82C4BAB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99442 Genomic DNA. Translation: CAA67805.1.
U17247 Genomic DNA. Translation: AAB67357.1.
BK006945 Genomic DNA. Translation: DAA09615.1.
PIRiS51438.
RefSeqiNP_013409.1. NM_001182194.1.

Genome annotation databases

EnsemblFungiiYLR306W; YLR306W; YLR306W.
GeneIDi851015.
KEGGisce:YLR306W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99442 Genomic DNA. Translation: CAA67805.1.
U17247 Genomic DNA. Translation: AAB67357.1.
BK006945 Genomic DNA. Translation: DAA09615.1.
PIRiS51438.
RefSeqiNP_013409.1. NM_001182194.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3O2UX-ray2.00A/B1-188[»]
3TDIX-ray2.30C/D1-24[»]
ProteinModelPortaliP52491.
SMRiP52491.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31571. 32 interactors.
DIPiDIP-2051N.
IntActiP52491. 1 interactor.
MINTiMINT-552826.

Proteomic databases

MaxQBiP52491.
PRIDEiP52491.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR306W; YLR306W; YLR306W.
GeneIDi851015.
KEGGisce:YLR306W.

Organism-specific databases

EuPathDBiFungiDB:YLR306W.
SGDiS000004297. UBC12.

Phylogenomic databases

GeneTreeiENSGT00630000089859.
HOGENOMiHOG000233456.
InParanoidiP52491.
KOiK10579.
OMAiYHPNIDI.
OrthoDBiEOG092C5L1U.

Enzyme and pathway databases

UniPathwayiUPA00885.
BioCyciYEAST:G3O-32394-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP52491.
PROiP52491.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiUBC12_YEAST
AccessioniPrimary (citable) accession number: P52491
Secondary accession number(s): D6VYU9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: November 2, 2016
This is version 142 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: 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.