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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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei115 – 1151Glycyl thioester intermediatePROSITE-ProRule annotation

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.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 188188NEDD8-conjugating enzyme UBC12PRO_0000082501Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionine1 Publication

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.
PeptideAtlasiP52491.

Interactioni

Subunit structurei

Interacts with DCN1.1 Publication

Protein-protein interaction databases

BioGridi31571. 32 interactions.
DIPiDIP-2051N.
IntActiP52491. 1 interaction.
MINTiMINT-552826.

Structurei

Secondary structure

188
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi1 – 1919Combined sources
Beta strandi20 – 223Combined sources
Helixi27 – 3711Combined sources
Beta strandi45 – 517Combined sources
Beta strandi63 – 686Combined sources
Beta strandi71 – 733Combined sources
Turni74 – 774Combined sources
Beta strandi80 – 856Combined sources
Turni88 – 925Combined sources
Beta strandi96 – 994Combined sources
Beta strandi112 – 1143Combined sources
Helixi117 – 1193Combined sources
Turni120 – 1223Combined sources
Helixi129 – 14113Combined sources
Helixi151 – 1588Combined sources
Helixi161 – 17212Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3O2UX-ray2.00A/B1-188[»]
3TDIX-ray2.30C/D1-24[»]
ProteinModelPortaliP52491.
SMRiP52491. Positions 1-188.
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.
OrthoDBiEOG7F51DN.

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
EntryMethodResolution (Å)ChainPositionsPDBsum
3O2UX-ray2.00A/B1-188[»]
3TDIX-ray2.30C/D1-24[»]
ProteinModelPortaliP52491.
SMRiP52491. Positions 1-188.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31571. 32 interactions.
DIPiDIP-2051N.
IntActiP52491. 1 interaction.
MINTiMINT-552826.

Proteomic databases

MaxQBiP52491.
PeptideAtlasiP52491.

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.
OrthoDBiEOG7F51DN.

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...

Publicationsi

« Hide 'large scale' publications
  1. "A novel protein modification pathway related to the ubiquitin system."
    Liakopoulos D., Doenges G., Matuschewski K., Jentsch S.
    EMBO J. 17:2208-2214(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
    Strain: ATCC 200912 / DF5.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
    , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex."
    Scott D.C., Monda J.K., Bennett E.J., Harper J.W., Schulman B.A.
    Science 334:674-678(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 2-24 IN COMPLEX WITH DCN1, ACETYLATION AT MET-1.

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: June 8, 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

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.