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UniProtKB - Q04228 (UBX2_YEAST)

Entry version 152 (02 Jun 2021)
Sequence version 1 (01 Nov 1997)
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Protein

UBX domain-containing protein 2

Gene

UBX2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Integral endoplasmic reticulum membrane protein that coordinates the assembly of the ER-associated protein degradation (ERAD) machinery at the ER membrane. Mediates binding of CDC48 to the E3 ubiquitin ligases SSM4/DOA10 and HRD1, and to ERAD substrates. Component of the DOA10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains. ERAD-C substrates are ubiquitinated through DOA10 in conjunction with the E2 ubiquitin-conjugating enzymes UBC6 and UBC7-CUE1. Also component of the HRD1 ubiquitin ligase complex, which is part of the ERAD-L and ERAD-M pathways responsible for the rapid degradation of soluble lumenal and membrane proteins with misfolded lumenal domains (ERAD-L), or ER-membrane proteins with misfolded transmembrane domains (ERAD-M). ERAD-L substrates are ubiquitinated through HRD1 in conjunction with the E2 ubiquitin-conjugating enzymes UBC1 and UBC7-CUE1. Ubiquitinated substrates are then removed to the cytosol via the action of the UFD1-NPL4-CDC48/p97 (UNC) AAA ATPase complex and targeted to the proteasome.

4 Publications

Miscellaneous

Present with 12600 molecules/cell in log phase SD medium.1 Publication

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processUbl conjugation pathway

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
UBX domain-containing protein 2
Alternative name(s):
Secretion lowering protein 1
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:UBX2
Synonyms:SEL1
Ordered Locus Names:YML013W
ORF Names:YM9571.05
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome XIII

Organism-specific databases

Saccharomyces Genome Database

More...SGDi		S000004475, UBX2

Eukaryotic Pathogen, Vector and Host Database Resources

More...VEuPathDBi		FungiDB:YML013W

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the subcellular compartment where each non-membrane region of a membrane-spanning protein is found.<p><a href='/help/topo_dom' target='_top'>More...</a></p>Topological domaini1 – 80CytoplasmicSequence analysisAdd BLAST80
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei81 – 101HelicalSequence analysisAdd BLAST21
Topological domaini102 – 151LumenalSequence analysisAdd BLAST50
Transmembranei152 – 172HelicalSequence analysisAdd BLAST21
Topological domaini173 – 584CytoplasmicSequence analysisAdd BLAST412

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002109991 – 584UBX domain-containing protein 2Add BLAST584

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		Q04228

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		Q04228

PRoteomics IDEntifications database

More...PRIDEi		Q04228

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		Q04228

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the DOA10 complex which contains SSM4/DOA10, CDC48, NPL4, UFD1 AND UBX2/SEL1. The complex is composed of the membrane integral E3 ligase SSM4/DOA10 and the heterotrimeric UFD1-NPL4-CDC48/p97 (UNC) ATPase complex recruited by UBX2/SEL1.

Component of the HRD1 complex which contains HRD1, HRD3, USA1, DER1, YOS9, KAR2, CDC48, NPL4, UFD1 AND UBX2/SEL1. The complex is composed of the core membrane complex, consisting of the E3 ligase HRD1 and its cofactors HRD3, DER1 and USA1, the substrate recruiting factors KAR2 and YOS9, and the heterotrimeric UFD1-NPL4-CDC48/p97 (UNC) ATPase complex recruited by UBX2/SEL1.

Interacts with CDC48.

4 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">Interaction</a>' section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Hide details

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		35156, 400 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-3070, HRD1 ubiquitin ligase complex
CPX-3074, Doa10 ubiquitin ligase complex

Database of interacting proteins

More...DIPi		DIP-5073N

Protein interaction database and analysis system

More...IntActi		Q04228, 16 interactors

Molecular INTeraction database

More...MINTi		Q04228

STRING: functional protein association networks

More...STRINGi		4932.YML013W

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...RNActi		Q04228, protein

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini426 – 570UBXAdd BLAST145

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG1363, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_414514_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q04228

Identification of Orthologs from Complete Genome Data

More...OMAi		RSEWNVQ

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR001012, UBX_dom

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00789, UBX, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00166, UBX, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q04228-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MPVVNHEDSE FHLSHTEEDK LNEFQVITNF PPEDLPDVVR LLRNHGWQLE 
        60         70         80         90        100
PALSRYFDGE WKGEPDQMGE PTQTSTPMAE TLVPPALGPR PLLFTASLPV 
       110        120        130        140        150
VRPLPANFRN DFRTIGLNGR SNTVWSMFES FSYDGNPFLF ILLLIPRIIN 
       160        170        180        190        200
RLSATIFTFF CTLLSLHSIS GGGNSGKPKI SKVPKAPTRE THIPLAEILG 
       210        220        230        240        250
DTKDKDAFCE LKSFKPDISF NEALRIAKEE FKFMLLILVG DTYDTDTDTV 
       260        270        280        290        300
DVNSKLLLEK ILLNKKTLQY LRKIDNDLII YLKCVHELEP WLVARQLGVR 
       310        320        330        340        350
NTPEIFLIAN VANKASHSET LPSQRLSILG KLKVNSLNRF LQSLTNVVEK 
       360        370        380        390        400
YTPELVVNKT EMHELRMSRE IKKLQEDAYK KSLEMDRIKA IEKEKSLKHA 
       410        420        430        440        450
QDLKLNSTAR QLKWLKACID EIQPFETTGK QATLQFRTSS GKRFVKKFPS 
       460        470        480        490        500
MTTLYQIYQS IGCHIYLAVY SSDPAEWSNA LQDKIRQLSA DDDMLCFKEG 
       510        520        530        540        550
QLETATATTI EELGHIINNE LTSFDLERGK LEFDFELVSP FPKYTVHPNE 
       560        570        580 
HMSVDQVPQL WPNGSLLVEA LDEEDEEDEE NEEQ
Length:584
Mass (Da):66,761
Last modified:November 1, 1997 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iDA4DDD3D624C17B8
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
Z49810 Genomic DNA Translation: CAA89939.1
BK006946 Genomic DNA Translation: DAA09885.1

Protein sequence database of the Protein Information Resource

More...PIRi		S55106

NCBI Reference Sequences

More...RefSeqi		NP_013699.1, NM_001182371.1

Genome annotation databases

Ensembl fungal genome annotation project

More...EnsemblFungii		YML013W_mRNA; YML013W; YML013W

Database of genes from NCBI RefSeq genomes

More...GeneIDi		854995

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		sce:YML013W

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49810 Genomic DNA Translation: CAA89939.1
BK006946 Genomic DNA Translation: DAA09885.1
PIRiS55106
RefSeqiNP_013699.1, NM_001182371.1

3D structure databases

Database of comparative protein structure models

More...ModBasei		Search...

SWISS-MODEL Interactive Workspace

More...SWISS-MODEL-Workspacei		Submit a new modelling project...

Protein-protein interaction databases

BioGRIDi35156, 400 interactors
ComplexPortaliCPX-3070, HRD1 ubiquitin ligase complex
CPX-3074, Doa10 ubiquitin ligase complex
DIPiDIP-5073N
IntActiQ04228, 16 interactors
MINTiQ04228
STRINGi4932.YML013W

PTM databases

iPTMnetiQ04228

Proteomic databases

MaxQBiQ04228
PaxDbiQ04228
PRIDEiQ04228

Genome annotation databases

EnsemblFungiiYML013W_mRNA; YML013W; YML013W
GeneIDi854995
KEGGisce:YML013W

Organism-specific databases

SGDiS000004475, UBX2
VEuPathDBiFungiDB:YML013W

Phylogenomic databases

eggNOGiKOG1363, Eukaryota
HOGENOMiCLU_414514_0_0_1
InParanoidiQ04228
OMAiRSEWNVQ

Miscellaneous databases

Protein Ontology

More...PROi		PR:Q04228
RNActiQ04228, protein

Family and domain databases

InterProiView protein in InterPro
IPR001012, UBX_dom
PfamiView protein in Pfam
PF00789, UBX, 1 hit
SMARTiView protein in SMART
SM00166, UBX, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiUBX2_YEAST
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q04228
Secondary accession number(s): D6VZG1
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: June 2, 2021
This is version 152 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names
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