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Protein

Polyubiquitin

Gene
N/A
Organism
Xenopus laevis (African clawed frog)
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 sitei69 – 691Activating enzyme
Sitei83 – 831Essential for function
Binding sitei87 – 871Activating enzyme

Names & Taxonomyi

Protein namesi
Recommended name:
Polyubiquitin
Cleaved into the following chain:
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini‹1 – 15›15UbiquitinPRO_0000114811Add
BLAST
Chaini16 – 9176UbiquitinPRO_0000396250Add
BLAST
Chaini92 – 16776UbiquitinPRO_0000396251Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki21 – 21Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki26 – 26Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki42 – 42Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki44 – 44Glycyl 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
Cross-linki78 – 78Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki91 – 91Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
CCNB1IP1Q9NPC32EBI-412964,EBI-745269From a different organism.

Protein-protein interaction databases

DIPiDIP-40040N.
IntActiP62972. 3 interactions.
MINTiMINT-5210721.

Structurei

Secondary structure

1
167
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi93 – 986Combined sources
Beta strandi103 – 1075Combined sources
Helixi114 – 12411Combined sources
Turni129 – 1313Combined sources
Beta strandi132 – 1365Combined sources
Turni147 – 1515Combined sources
Beta strandi157 – 1637Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2K39NMR-A92-167[»]
2KDENMR-B/C92-167[»]
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62972.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini‹1 – 15›15Ubiquitin-like 1PROSITE-ProRule annotationAdd
BLAST
Domaini16 – 9176Ubiquitin-like 2PROSITE-ProRule annotationAdd
BLAST
Domaini92 – 16776Ubiquitin-like 3PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the ubiquitin family.Curated
Contains 3 ubiquitin-like domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Family and domain databases

InterProiIPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF00240. ubiquitin. 2 hits.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 2 hits.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 2 hits.
PROSITEiPS00299. UBIQUITIN_1. 2 hits.
PS50053. UBIQUITIN_2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Fragment.

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

P62972-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
QKESTLHLVL RLRGGMQIFV KTLTGKTITL EVEPSDTIEN VKAKIQDKEG
60 70 80 90 100
IPPDQQRLIF AGKQLEDGRT LSDYNIQKES TLHLVLRLRG GMQIFVKTLT
110 120 130 140 150
GKTITLEVEP SDTIENVKAK IQDKEGIPPD QQRLIFAGKQ LEDGRTLSDY
160
NIQKESTLHL VLRLRGG
Length:167
Mass (Da):18,801
Last modified:August 10, 2010 - v2
Checksum:i9C8F431544081131
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Non-terminal residuei1 – 11

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M11512 mRNA. Translation: AAA49978.1.
UniGeneiXl.4135.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M11512 mRNA. Translation: AAA49978.1.
UniGeneiXl.4135.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2K39NMR-A92-167[»]
2KDENMR-B/C92-167[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-40040N.
IntActiP62972. 3 interactions.
MINTiMINT-5210721.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP62972.

Family and domain databases

InterProiIPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF00240. ubiquitin. 2 hits.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 2 hits.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 2 hits.
PROSITEiPS00299. UBIQUITIN_1. 2 hits.
PS50053. UBIQUITIN_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiUBIQP_XENLA
AccessioniPrimary (citable) accession number: P62972
Secondary accession number(s): P02248
, P02249, P02250, Q29120, Q91887, Q91888
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: August 10, 2010
Last modified: September 16, 2015
This is version 63 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Ubiquitin is synthesized as a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species (up to 12 in Xenopus). In some species there is a final amino-acid after the last repeat. Some ubiquitin genes contain a single copy of ubiquitin fused to a ribosomal protein (either L40 or S27a).
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

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.