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UniProtKB - P39998 (EDC3_YEAST)

Entry version 154 (07 Oct 2020)
Sequence version 1 (01 Feb 1995)
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Protein

Enhancer of mRNA-decapping protein 3

Gene

EDC3

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

Stimulates decapping of both stable and unstable mRNA during mRNA decay. Does not affect nonsense-mediated mRNA decay. Required for normal P-body assembly.2 Publications

Miscellaneous

Present with 2340 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

  • mRNA binding Source: SGD
Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-SCE-430039, mRNA decay by 5' to 3' exoribonuclease

<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:
Enhancer of mRNA-decapping protein 3
<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:EDC3
Synonyms:LSM16
Ordered Locus Names:YEL015W
<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 V

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...EuPathDBi		FungiDB:YEL015W

Saccharomyces Genome Database

More...SGDi		S000000741, EDC3

<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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

<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>Keywords - Cellular componenti

Cytoplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi360 – 361RH → AA: Abolishes homodimerization. 1 Publication2

<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_00002026131 – 551Enhancer of mRNA-decapping protein 3Add BLAST551

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei257PhosphoserineCombined sources1
Modified residuei261PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		P39998

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

More...PaxDbi		P39998

PRoteomics IDEntifications database

More...PRIDEi		P39998

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		P39998

<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

Homodimer.

Interacts with DCP2.

1 Publication

<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		36716, 90 interactors

Database of interacting proteins

More...DIPi		DIP-842N

Protein interaction database and analysis system

More...IntActi		P39998, 24 interactors

Molecular INTeraction database

More...MINTi		P39998

STRING: functional protein association networks

More...STRINGi		4932.YEL015W

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...RNActi		P39998, 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

Secondary structure

1551
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P39998

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

<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>Domaini93 – 129DFDFPROSITE-ProRule annotationAdd BLAST37
Domaini288 – 527YjeF N-terminalPROSITE-ProRule annotationAdd BLAST240

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the EDC3 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG2585, Eukaryota

Ensembl GeneTree

More...GeneTreei		ENSGT00390000016435

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_037134_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P39998

KEGG Orthology (KO)

More...KOi		K12615

Identification of Orthologs from Complete Genome Data

More...OMAi		NLAMFDK

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.40.50.10260, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR025762, DFDF
IPR019050, FDF_dom
IPR004443, YjeF_N_dom
IPR036652, YjeF_N_dom_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF09532, FDF, 1 hit
PF03853, YjeF_N, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM01199, FDF, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF64153, SSF64153, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS51512, DFDF, 1 hit
PS51385, YJEF_N, 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.

P39998-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSQFVGFGVQ VELKDGKLIQ GKIAKATSKG LTLNDVQFGD GGKSQAFKVR 
        60         70         80         90        100
ASRLKDLKVL TVASQSGKRK QQRQQQQQND YNQNRGEHID WQDDDVSKIK 
       110        120        130        140        150
QQEDFDFQRN LGMFNKKDVF AQLKQNDDIL PENRLQGHNR KQTQLQQNNY 
       160        170        180        190        200
QNDELVIPDA KKDSWNKISS RNEQSTHQSQ PQQDAQDDLV LEDDEHEYDV 
       210        220        230        240        250
DDIDDPKYLP ITQSLNITHL IHSATNSPSI NDKTKGTVIN DKDQVLAKLG 
       260        270        280        290        300
QMIISQSRSN STSLPAANKQ TTIRSKNTKQ NIPMATPVQL LEMESITSEF 
       310        320        330        340        350
FSINSAGLLE NFAVNASFFL KQKLGGRARL RLQNSNPEPL VVILASDSNR 
       360        370        380        390        400
SGAKALALGR HLCQTGHIRV ITLFTCSQNE LQDSMVKKQT DIYKKCGGKI 
       410        420        430        440        450
VNSVSSLESA METLNSPVEI VIDAMQGYDC TLSDLAGTSE VIESRIKSMI 
       460        470        480        490        500
SWCNKQRGST KVWSLDIPNG FDAGSGMPDI FFSDRIEATG IICSGWPLIA 
       510        520        530        540        550
INNLIANLPS LEDAVLIDIG IPQGAYSQRT SLRKFQNCDL FVTDGSLLLD 

L
Length:551
Mass (Da):61,340
Last modified:February 1, 1995 - 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:iBF28AE67F9303A73
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
U18530 Genomic DNA Translation: AAB64492.1
BK006939 Genomic DNA Translation: DAA07639.1

Protein sequence database of the Protein Information Resource

More...PIRi		S50444

NCBI Reference Sequences

More...RefSeqi		NP_010901.1, NM_001178830.1

Genome annotation databases

Ensembl fungal genome annotation project

More...EnsemblFungii		YEL015W_mRNA; YEL015W; YEL015W

Database of genes from NCBI RefSeq genomes

More...GeneIDi		856700

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		sce:YEL015W

<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
U18530 Genomic DNA Translation: AAB64492.1
BK006939 Genomic DNA Translation: DAA07639.1
PIRiS50444
RefSeqiNP_010901.1, NM_001178830.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4BRUX-ray3.24B77-116[»]
6Y3ZX-ray3.49C1-66[»]
SMRiP39998
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi36716, 90 interactors
DIPiDIP-842N
IntActiP39998, 24 interactors
MINTiP39998
STRINGi4932.YEL015W

PTM databases

iPTMnetiP39998

Proteomic databases

MaxQBiP39998
PaxDbiP39998
PRIDEiP39998

Genome annotation databases

EnsemblFungiiYEL015W_mRNA; YEL015W; YEL015W
GeneIDi856700
KEGGisce:YEL015W

Organism-specific databases

EuPathDBiFungiDB:YEL015W
SGDiS000000741, EDC3

Phylogenomic databases

eggNOGiKOG2585, Eukaryota
GeneTreeiENSGT00390000016435
HOGENOMiCLU_037134_0_0_1
InParanoidiP39998
KOiK12615
OMAiNLAMFDK

Enzyme and pathway databases

ReactomeiR-SCE-430039, mRNA decay by 5' to 3' exoribonuclease

Miscellaneous databases

Protein Ontology

More...PROi		PR:P39998
RNActiP39998, protein

Family and domain databases

Gene3Di3.40.50.10260, 1 hit
InterProiView protein in InterPro
IPR025762, DFDF
IPR019050, FDF_dom
IPR004443, YjeF_N_dom
IPR036652, YjeF_N_dom_sf
PfamiView protein in Pfam
PF09532, FDF, 1 hit
PF03853, YjeF_N, 1 hit
SMARTiView protein in SMART
SM01199, FDF, 1 hit
SUPFAMiSSF64153, SSF64153, 1 hit
PROSITEiView protein in PROSITE
PS51512, DFDF, 1 hit
PS51385, YJEF_N, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

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 nameiEDC3_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: P39998
Secondary accession number(s): D3DLN5
<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: February 1, 1995
Last sequence update: February 1, 1995
Last modified: October 7, 2020
This is version 154 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

3D-structure, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome V
    Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families
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