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Protein

Polyubiquitin-C

Gene

Ubc

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei130 – 1301Activating enzymeBy similarity
Sitei144 – 1441Essential for functionBy similarity
Binding sitei148 – 1481Activating enzymeBy similarity

GO - Biological processi

  • ubiquitin-dependent protein catabolic process Source: RGD
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Polyubiquitin-C
Cleaved into the following 2 chains:
Gene namesi
Name:Ubc
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi621244. Ubc.

Subcellular locationi

Ubiquitin :

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7676UbiquitinPRO_5000139688Add
BLAST
Chaini77 – 15276UbiquitinPRO_5000139689Add
BLAST
Chaini153 – 22876UbiquitinPRO_5000139690Add
BLAST
Chaini229 – 30476UbiquitinPRO_5000139691Add
BLAST
Chaini305 – 38076UbiquitinPRO_5000139692Add
BLAST
Chaini381 – 45676UbiquitinPRO_5000139693Add
BLAST
Chaini457 – 53276UbiquitinPRO_5000139694Add
BLAST
Chaini533 – 60876UbiquitinPRO_5000139695Add
BLAST
Chaini609 – 68476UbiquitinPRO_5000139696Add
BLAST
Chaini685 – 76076UbiquitinPRO_5000139697Add
BLAST
Chaini761 – 81050Ubiquitin-relatedPRO_5000139698Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki27 – 27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei65 – 651Phosphoserine; by PINK1By similarity
Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation
Modified residuei141 – 1411PhosphoserineBy similarity

Post-translational modificationi

Ubiquitin: Phosphorylated at Ser-65 by PINK1 during mitophagy. Phosphorylated ubiquitin specifically binds and activates parkin (PARK2), triggering mitophagy. Phosphorylation does not affect E1-mediated E2 charging of ubiquitin but affects discharging of E2 enzymes to form polyubiquitin chains. It also affects deubiquitination by deubiquitinase enzymes such as USP30.By similarity

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ63429.
PRIDEiQ63429.

PTM databases

iPTMnetiQ63429.
PhosphoSiteiQ63429.

Interactioni

Protein-protein interaction databases

BioGridi248372. 817 interactions.
IntActiQ63429. 1 interaction.
STRINGi10116.ENSRNOP00000043934.

Structurei

3D structure databases

ProteinModelPortaliQ63429.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7676Ubiquitin-like 1PROSITE-ProRule annotationAdd
BLAST
Domaini77 – 15276Ubiquitin-like 2PROSITE-ProRule annotationAdd
BLAST
Domaini153 – 22876Ubiquitin-like 3PROSITE-ProRule annotationAdd
BLAST
Domaini229 – 30476Ubiquitin-like 4PROSITE-ProRule annotationAdd
BLAST
Domaini305 – 38076Ubiquitin-like 5PROSITE-ProRule annotationAdd
BLAST
Domaini381 – 45676Ubiquitin-like 6PROSITE-ProRule annotationAdd
BLAST
Domaini457 – 53276Ubiquitin-like 7PROSITE-ProRule annotationAdd
BLAST
Domaini533 – 60876Ubiquitin-like 8PROSITE-ProRule annotationAdd
BLAST
Domaini609 – 68476Ubiquitin-like 9PROSITE-ProRule annotationAdd
BLAST
Domaini685 – 76076Ubiquitin-like 10PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the ubiquitin family.Curated
Contains 10 ubiquitin-like domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0001. Eukaryota.
COG5272. LUCA.
HOGENOMiHOG000233942.
HOVERGENiHBG000057.
InParanoidiQ63429.
KOiK08770.
PhylomeDBiQ63429.

Family and domain databases

InterProiIPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF00240. ubiquitin. 10 hits.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 10 hits.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 10 hits.
PROSITEiPS00299. UBIQUITIN_1. 10 hits.
PS50053. UBIQUITIN_2. 10 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q63429-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLSDYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVEPSDTIE
110 120 130 140 150
NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLSDYNIQKE STLHLVLRLR
160 170 180 190 200
GGMQIFVKTL TGKTITLEVE PSDTIENVKA KIQDKEGIPP DQQRLIFAGK
210 220 230 240 250
QLEDGRTLSD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVEPSDT
260 270 280 290 300
IENVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLSDYNIQ KESTLHLVLR
310 320 330 340 350
LRGGMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA
360 370 380 390 400
GKQLEDGRTL SDYNIQKEST LHLVLRLRGG MQIFVKTLTG KTITLEVEPS
410 420 430 440 450
DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV
460 470 480 490 500
LRLRGGMQIF VKTLTGKTIT LEVEPSDTIE NVKAKIQDKE GIPPDQQRLI
510 520 530 540 550
FAGKQLEDGR TLSDYNIQKE STLHLVLRLR GGMQIFVKTL TGKTITLEVE
560 570 580 590 600
PSDTIENVKA KIQDKEGIPP DQQRLIFAGK QLEDGRTLSD YNIQKESTLH
610 620 630 640 650
LVLRLRGGMQ IFVKTLTGKT ITLEVEPSDT IENVKAKIQD KEGIPPDQQR
660 670 680 690 700
LIFAGKQLED GRTLSDYNIQ KESTLHLVLR LRGGMQIFVK TLTGKTITLE
710 720 730 740 750
VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST
760 770 780 790 800
LHLVLRLRGG MQIFVKTLTG KTITLEVEPS VNTKKVKQED TRTFLTTVSR
810
KSPSCACSWV
Length:810
Mass (Da):91,087
Last modified:November 1, 1996 - v1
Checksum:i4D4ADB697ADA3315
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti776 – 7761E → D in AAI03478 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D17296 mRNA. Translation: BAA04129.1.
BC103477 mRNA. Translation: AAI03478.1.
PIRiS45359.
RefSeqiNP_059010.1. NM_017314.1.
UniGeneiRn.3761.

Genome annotation databases

GeneIDi50522.
KEGGirno:50522.
UCSCiRGD:621244. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D17296 mRNA. Translation: BAA04129.1.
BC103477 mRNA. Translation: AAI03478.1.
PIRiS45359.
RefSeqiNP_059010.1. NM_017314.1.
UniGeneiRn.3761.

3D structure databases

ProteinModelPortaliQ63429.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi248372. 817 interactions.
IntActiQ63429. 1 interaction.
STRINGi10116.ENSRNOP00000043934.

PTM databases

iPTMnetiQ63429.
PhosphoSiteiQ63429.

Proteomic databases

PaxDbiQ63429.
PRIDEiQ63429.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi50522.
KEGGirno:50522.
UCSCiRGD:621244. rat.

Organism-specific databases

CTDi7316.
RGDi621244. Ubc.

Phylogenomic databases

eggNOGiKOG0001. Eukaryota.
COG5272. LUCA.
HOGENOMiHOG000233942.
HOVERGENiHBG000057.
InParanoidiQ63429.
KOiK08770.
PhylomeDBiQ63429.

Miscellaneous databases

NextBioi610320.
PROiQ63429.

Family and domain databases

InterProiIPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF00240. ubiquitin. 10 hits.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 10 hits.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 10 hits.
PROSITEiPS00299. UBIQUITIN_1. 10 hits.
PS50053. UBIQUITIN_2. 10 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence and expression of the rat polyubiquitin mRNA."
    Hayashi T., Noga M., Matsuda M.
    Biochim. Biophys. Acta 1218:232-234(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: Wistar.
    Tissue: Brain cortex and Hippocampus.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 381-810.
    Tissue: Prostate.
  3. "Differential feeding-related regulation of ubiquitin and calbindin9kDa in rat duodenum."
    Hubbard M.J., Carne A.
    Biochim. Biophys. Acta 1200:191-196(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-76.
    Strain: Wistar.
    Tissue: Duodenum.
  4. Lubec G., Diao W., Kang S.U.
    Submitted (JUL-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 30-42 AND 55-72, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: Sprague-Dawley.
    Tissue: Brain and Hippocampus.

Entry informationi

Entry nameiUBC_RAT
AccessioniPrimary (citable) accession number: Q63429
Secondary accession number(s): Q3ZBA1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: November 1, 1996
Last modified: January 20, 2016
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Ubiquitin is encoded by 4 different genes. Uba52 and Rps27a genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.
For the sake of clarity sequence features are annotated only for the first chain, and are not repeated for each of the following chains.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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.