ubc4 (SPBC119.02)


Gene Standard Nameubc4 Characterisation Statuspublished
Systematic IDSPBC119.02 Feature Typeprotein coding
SynonymsubcP1 Name Description
Productubiquitin conjugating enzyme E2 Ubc4/UbcP1 Product Size147aa, 16.48 kDa
Genomic Location Chromosome II, 715227-716311 (1085nt); CDS:715333-716226 (894nt)

Ensembl Gene Location
GO Molecular Function
Term NameCount
ATP binding560
Annotation ExtensionEvidenceWith/FromReference
protein binding872
Annotation ExtensionEvidenceWith/FromReference
ubiquitin conjugating enzyme activity12
Annotation ExtensionEvidenceWith/FromReference
GO Biological Process
Term NameCount
positive regulation of mitotic metaphase/anaphase transition52
Annotation ExtensionEvidenceWith/FromReference
protein localization to Golgi apparatus13
Annotation ExtensionEvidenceWith/FromReference
protein polyubiquitination8
Annotation ExtensionEvidenceWith/FromReference
protein processing38
Annotation ExtensionEvidenceWith/FromReference
protein ubiquitination involved in ubiquitin-dependent protein catabolic process17
Annotation ExtensionEvidenceWith/FromReference
regulation of protein glycosylation4
Annotation ExtensionEvidenceWith/FromReference
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process6
Annotation ExtensionEvidenceWith/FromReference
sterol regulatory element binding protein cleavage8
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
cytoplasm4212
Annotation ExtensionEvidenceWith/FromReference
cytosol2302
Annotation ExtensionEvidenceWith/FromReference
nuclear SCF ubiquitin ligase complex5
Annotation ExtensionEvidenceWith/FromReference
nucleus2691
Annotation ExtensionEvidenceWith/FromReference
FYPO Single-Allele Phenotypes
Gene Deletion Viability: Inviable

Population Phenotype

Term NameGenotypesCount
decreased cell population growth at high temperatureubc4-P61S (P61S)173
inviable vegetative cell populationΔubcP1 (1-87)1452
ubc4Δ
normal vegetative cell population growthubc4-P61S (P61S)851

Cell Phenotype

Term NameGenotypesCount
abnormal cell cycle arrest in mitotic metaphaseΔubcP1 (1-87)15
abnormal mitotic cell cycleubc4Δ882
abnormal protein glycosylation19
affecting dsc1ubc4-P61S (P61S)
abolished protein ubiquitination11
affecting ubc4L10D (L10D)
cutΔubcP1 (1-87)128
decreased anaphase-promoting complex-dependent protein catabolic process3
affecting cut2ubc4-P61S (P61S)
affecting cdc13ubc4-P61S (P61S)
decreased protein degradation during mitosis2
affecting cdc13ΔubcP1 (1-87)
affecting cdc13ubc4-P61S (P61S)
decreased protein localization to Golgi apparatus, with protein mislocalized to endoplasmic reticulum5
affects localization of dsc2ubc4-P61S (P61S)
decreased protein polyubiquitination2
affecting cdc13ubc4-P61S (P61S)
decreased protein processing15
affecting sre2ubc4-P61S (P61S)
decreased protein ubiquitination8
affecting ubc4N79Y,L119A (N79Y, L119A)
affecting ubc4L30A,F31A (L30A, F31A)
affecting ubc4D28A (D28A)
affecting ubc4D116A (D116A)
affecting ubc4A124F (A124F)
affecting ubc4N7D (N7D)
affecting ubc4P118A (P118A)
affecting ubc4L30A (L30A)
affecting ubc4P121A (P121A)
affecting ubc4N79A (N79A)
affecting ubc4L119A (L119A)
affecting ubc4D28R (D28R)
incomplete mitotic sister chromatid segregation, with unseparated DNAΔubcP1 (1-87)10
increased protein level during mitotic G1 phase2
affecting cdc13ΔubcP1 (1-87)
inviable after spore germination, without cell divisionubc4Δ495
inviable vegetative cellΔubcP1 (1-87)1352
normal anaphase-promoting complex-dependent protein catabolic process3
affecting slp1ubc4-P61S (P61S)
normal Dsc complex assemblyubc4-P61S (P61S)3
normal protein ubiquitination6
affecting ubc4H125A (H125A)
affecting ubc4S108D (S108D)
affecting ubc4R90A (R90A)
affecting ubc4S108A (S108A)
affecting ubc4K128A (K128A)
viable elongated vegetative cellubc4Δ320
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in ptr3 ubiquitin activating enzyme E1
FYPO affected by mutation in ubc4 ubiquitin conjugating enzyme E2 Ubc4/UbcP1
GO substrate of ptr3 ubiquitin activating enzyme E1
GO substrate of sst2 human AMSH/STAMBP protein homolog, ubiquitin specific-protease
GO substrate of ubp15 ubiquitin C-terminal hydrolase Ubp15
GO substrate of ubp4 ubiquitin C-terminal hydrolase Ubp4
GO substrate of ubp5 ubiquitin C-terminal hydrolase Ubp5
GO substrate of ubp9 ubiquitin C-terminal hydrolase Ubp9
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons715227..715452, 715532..715609, 715981..716311
Intron715453..715531, 715610..715980
mRNA715227..716311
5' UTR715227..715332PMID:21511999
CDS715333..715452, 715532..715609, 715981..716226
3' UTR716227..716311PMID:21511999
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF00179 Pfam IPR000608 Ubiquitin-conjugating enzyme E2 5 141 14
SM00212 SMART 4 147 14
PS00183 Prosite Patterns IPR023313 Ubiquitin-conjugating enzyme, active site 74 89 10
PS50127 Prosite Profiles IPR000608 Ubiquitin-conjugating enzyme E2 4 136 14
PTHR24068 HMMPANTHER 1 147 2
3.10.110.10 Gene3D IPR016135 Ubiquitin-conjugating enzyme/RWD-like 1 146 19
SSF54495 SuperFamily IPR016135 Ubiquitin-conjugating enzyme/RWD-like 1 146 19

View domain organization at Pfam

Protein Properties

Ave. residue weight 112.08 Da
Charge 1.00
Codon Adaptation Index 0.46
Isoelectric point 6.93
Molecular weight 16.48 kDa
Number of residues 147
Modifications

Protein Modifications

Term NameResidueCount
ubiquitinylated lysineK15 512
Annotation ExtensionEvidenceResidueReference
IDA PMID:26412298
mass spectrometry evidence K15 PMID:26412298
Sequence
Gene Expression

Quantitative Gene Expression

View graphical display of gene expression data for ubc4 (SPBC119.02)

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
306990during GO:0000080PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
315701during GO:0000084PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
283788during GO:0000085PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
339257during GO:0000087PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
42054.17during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
305467during GO:0072690PECO:0000005,
PECO:0000126
single cellmass spectrometry evidencePMID:24763107
33683.72during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
52during GO:0072690PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
8during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000127,
PECO:0000014,
PECO:0000005
population wideexperimental evidencePMID:23101633
Taxonomic Conservation
DescriptionQualifierReferenceCount
conserved in fungi4606
conserved in eukaryotes4516
conserved in metazoa3424
conserved in vertebrates3399
conserved in eukaryotes only2505
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

Load genes that interact physically with SPBC119.02 into the Query Builder
View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
forms complex withapc11anaphase-promoting complex ubiquitin -protein ligase E3 subunit Apc11 Reconstituted ComplexPMID:21389117
forms complex withfbh1DNA helicase I, ubiquitin ligase F-box adaptor Fbh1 Reconstituted ComplexPMID:25165823
forms complex withdsc1Golgi Dsc E3 ligase complex subunit Dsc1 Reconstituted ComplexPMID:25918164
binds activation domain construct withSPBC36B7.05cubiquitin-protein ligase E3/phosphatidylinositol(3)-phosphate binding protein (predicted) Two-hybridPMID:26771498
binds activation domain construct withmeu23mug2/mug135/meu2 family Two-hybridPMID:26771498
binds activation domain construct withpub3HECT-type ubiquitin-protein ligase E3 Pub3 (predicted) Two-hybridPMID:26771498
modified byptr3ubiquitin activating enzyme E1 Biochemical ActivityPMID:23416107
affinity captured bycul3cullin 3 Affinity Capture-MSPMID:14527422
co-locates (via crystalisation or NMR) withptr3ubiquitin activating enzyme E1 Co-crystal or NMR structurePMID:23416107
Genetic Interactions

Source: BioGRID

Load genes that interact genetically with SPBC119.02 into the Query Builder
View these interactions in esyN

Gene Product Evidence Reference
rescuescia1histone chaperone Cia1 Phenotypic SuppressionPMID:21324894
rescuescdc42Rho family GTPase Cdc42 Phenotypic SuppressionPMID:10628977
synthetic growth defect withcia1histone chaperone Cia1 Synthetic Growth DefectPMID:21324894
overexpression rescuesapm1AP-1 adaptor complex mu subunit Apm1 Dosage RescuePMID:24454826
overexpression rescuesecm33cell wall protein Ecm33 Dosage RescuePMID:24454826
overexpression rescuescis4cation diffusion family zinc transmembrane transporter Cis4 Dosage RescuePMID:24454826
phenotype enhanced byubc11ubiquitin conjugating enzyme E2, Ubc11/UbcP4 Phenotypic EnhancementPMID:23442800
synthetically rescuesspc7NMS complex subunit, Spc105/KNL-1 family member, blinkin, Spc7 Synthetic RescuePMID:24497846
synthetically rescuesmis6kinetochore protein, CENP-I ortholog Mis6 Synthetic RescuePMID:24497846
synthetically rescuesmal2kinetochore protein, CENP-O ortholog Mal2 Synthetic RescuePMID:24497846
External References
Database Identifier Description
NBRP SPBC119.02 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC119.02 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC119.02 BioGRID Interaction Datasets
Expression Viewer SPBC119.02 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC119.02 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC119.02 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC119.02 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC119.02 Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC119.02 Transcriptome Viewer (Bähler Lab)
GEO SPBC119.02 GEO profiles
PInt SPBC119.02 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC119.02 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC119.02 Fission yeast phenotypic data & analysis
Cyclebase SPBC119.02.1 Cell Cycle Data
SPD / RIKEN32/32A10Orfeome Localization Data
IntEnz6.3.2.19Integrated relational Enzyme database
Rhea6.3.2.19Annotated reactions database
UniProtKB/SwissProtP46595Ubiquitin-conjugating enzyme E2 4
ModBaseP46595Database of comparative protein structure models
STRINGP46595Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_595283ubiquitin conjugating enzyme Ubc4
RefSeq mRNANM_001021190972h- ubiquitin conjugating enzyme Ubc4 (ubc4), mRNA
European Nucleotide ArchiveL37384ENA EMBL mapping
ePDB4II2The European PDB
PDB4II2PDB
PDBsum4II2PDBsum
European Nucleotide ArchiveCAA17917.1ENA Protein Mapping
MetaCycPWY-7511Protein ubiquitylation
UniParcUPI0000137961UniProt Archive
UniPathwayUPA00143Protein modification; protein ubiquitination

Literature for ubc4

Search: Europe PMC or PubMed

Release Version: PomBase:30_60 - 12 May 2016