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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)DescriptionActionsGraphical viewLength
Binding sitei130Activating enzymeBy similarity1
Sitei144Essential for functionBy similarity1
Binding sitei148Activating enzymeBy similarity1

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)DescriptionActionsGraphical viewLength
ChainiPRO_50001396881 – 76UbiquitinAdd BLAST76
ChainiPRO_500013968977 – 152UbiquitinAdd BLAST76
ChainiPRO_5000139690153 – 228UbiquitinAdd BLAST76
ChainiPRO_5000139691229 – 304UbiquitinAdd BLAST76
ChainiPRO_5000139692305 – 380UbiquitinAdd BLAST76
ChainiPRO_5000139693381 – 456UbiquitinAdd BLAST76
ChainiPRO_5000139694457 – 532UbiquitinAdd BLAST76
ChainiPRO_5000139695533 – 608UbiquitinAdd BLAST76
ChainiPRO_5000139696609 – 684UbiquitinAdd BLAST76
ChainiPRO_5000139697685 – 760UbiquitinAdd BLAST76
ChainiPRO_5000139698761 – 810Ubiquitin-relatedAdd BLAST50

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei65Phosphoserine; by PINK1By similarity1
Cross-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation
Cross-linki82Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki87Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki105Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki124Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki139Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei141PhosphoserineBy similarity1

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.
PhosphoSitePlusiQ63429.

Interactioni

Protein-protein interaction databases

BioGridi248372. 817 interactors.
IntActiQ63429. 1 interactor.
STRINGi10116.ENSRNOP00000043934.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5L9Uelectron microscopy6.40S1-78[»]
ProteinModelPortaliQ63429.
SMRiQ63429.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 76Ubiquitin-like 1PROSITE-ProRule annotationAdd BLAST76
Domaini77 – 152Ubiquitin-like 2PROSITE-ProRule annotationAdd BLAST76
Domaini153 – 228Ubiquitin-like 3PROSITE-ProRule annotationAdd BLAST76
Domaini229 – 304Ubiquitin-like 4PROSITE-ProRule annotationAdd BLAST76
Domaini305 – 380Ubiquitin-like 5PROSITE-ProRule annotationAdd BLAST76
Domaini381 – 456Ubiquitin-like 6PROSITE-ProRule annotationAdd BLAST76
Domaini457 – 532Ubiquitin-like 7PROSITE-ProRule annotationAdd BLAST76
Domaini533 – 608Ubiquitin-like 8PROSITE-ProRule annotationAdd BLAST76
Domaini609 – 684Ubiquitin-like 9PROSITE-ProRule annotationAdd BLAST76
Domaini685 – 760Ubiquitin-like 10PROSITE-ProRule annotationAdd BLAST76

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)DescriptionActionsGraphical viewLength
Sequence conflicti776E → D in AAI03478 (PubMed:15489334).Curated1

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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5L9Uelectron microscopy6.40S1-78[»]
ProteinModelPortaliQ63429.
SMRiQ63429.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi248372. 817 interactors.
IntActiQ63429. 1 interactor.
STRINGi10116.ENSRNOP00000043934.

PTM databases

iPTMnetiQ63429.
PhosphoSitePlusiQ63429.

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

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...

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: November 30, 2016
This is version 98 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.