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Entry version 98 (02 Dec 2020)
Sequence version 1 (24 May 2005)
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Protein

DNA repair endonuclease XPF

Gene

ercc4

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score:

Annotation score:4 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>
-Protein inferred from homologyi <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

Structure-specific DNA repair endonuclease responsible for the 5-prime incision during DNA repair. Involved in homologous recombination that assists in removing interstrand cross-link (By similarity).By similarity

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+By similarity

<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

GO - Biological processi

<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

Molecular functionDNA-binding, Endonuclease, Hydrolase, Nuclease
Biological processDNA damage, DNA repair
LigandMagnesium

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-DDI-5696395, Formation of Incision Complex in GG-NER
R-DDI-6782135, Dual incision in TC-NER

<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:
DNA repair endonuclease XPF (EC:3.1.-.-)
Alternative name(s):
DNA excision repair protein ERCC-4
<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:ercc4
ORF Names:DDB_G0284419
<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>OrganismiDictyostelium discoideum (Slime mold)
<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 identifieri44689 [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 lineageiEukaryotaAmoebozoaEvoseaEumycetozoaDictyosteliaDictyostelialesDictyosteliaceaeDictyostelium
<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
  • UP000002195 <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> Componentsi: Chromosome 4, Unassembled WGS sequence

Organism-specific databases

Dictyostelium discoideum online informatics resource

More...
dictyBasei
DDB_G0284419, xpf

<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

Keywords - Cellular componenti

Nucleus

<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_00003313681 – 964DNA repair endonuclease XPFAdd BLAST964

Proteomic databases

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

More...
PaxDbi
Q54PN5

<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

Heterodimer composed of ercc1 and xpf/ercc4.

By similarity

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
44689.DDB0232364

<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

3D structure databases

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

More...
SMRi
Q54PN5

Database of comparative protein structure models

More...
ModBasei
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>Domaini739 – 819ERCC4Add BLAST81

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi371 – 378Poly-Ser8
Compositional biasi461 – 481Poly-AsnAdd BLAST21
Compositional biasi566 – 576Poly-AsnAdd BLAST11
Compositional biasi728 – 736Poly-Gln9

<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 XPF family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG0442, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_002265_2_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q54PN5

Identification of Orthologs from Complete Genome Data

More...
OMAi
FHKILQA

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q54PN5

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR006166, ERCC4_domain
IPR011335, Restrct_endonuc-II-like
IPR010994, RuvA_2-like

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02732, ERCC4, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00891, ERCC4, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF47781, SSF47781, 1 hit
SSF52980, SSF52980, 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.

Q54PN5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSLEFYKQIF EDCLNDDGLV VMGSGLGIHN IILGFLKFYS DTDDLVLFLD
60 70 80 90 100
CQSNESLQNS YLFYHERLLN FGIKYSNLPT MVNVETVSSS TKTNMYSKGG
110 120 130 140 150
VYFGASSIFV LDYLTKRMPC NLVSGIIIQN AHRITDTSIE YLLIKLFRQN
160 170 180 190 200
NKKGFIKAFT TEPSLLVDEI GKLQRTMKYL HLKKLFLWPR FHQHISLILD
210 220 230 240 250
KHPPDLVELS IGMTNSMKRI EESLHLNTQR CISSLIAINK LPRLNGGNGG
260 270 280 290 300
NDSDSFEQIL KQQLKPMWSK LNLHSKQLVS SIKLLNQLKN NLLVYDCVTF
310 320 330 340 350
YSLLLYIQAS SDSLKEGLHT NSNYVDEVQP WLESKEAQNL FSASQERVYR
360 370 380 390 400
FKKLNSLKSP PKKLKTINND SSSSSSSSNL EKILTLEDNP KWNVLYQILQ
410 420 430 440 450
EIEEDKEKQG TILIFVKDET TVNQLSTYLD YGGYSFLLGK YEKLCSNQQY
460 470 480 490 500
LDELRKKKEE NNNNNNSNNN NNNNNNNNNN NSVKSLSSND NGGYSRYRRT
510 520 530 540 550
KNFKDNRKQQ IIETSKKKKG KGGTNDQNLF NMGIQLVDGH NKLNIPNPKF
560 570 580 590 600
INQDGSGGGG DNGDENNNNN NNLNINDGLT IASMNEEING LNDFYELLSP
610 620 630 640 650
PYIVIHPISK SLTILDEIRP TFIIVYDPDI SITRQIEVYK AENPGTPVRL
660 670 680 690 700
YFMTYSDSSE EYQYISKLQR EKSSFEKLIR EKTNLIIDTE QEGKIQLVDN
710 720 730 740 750
SKLELLDDMK STRNSRLGGL MKNFDSIQQQ QQQQQQKKTI IIDSHEFKSS
760 770 780 790 800
LPVVLHNNGY EIIPLRLEVG DFVLSPIHCI ERKSVSDLIG SFNSGRLFTQ
810 820 830 840 850
IEAMNRIYKN PILLIEFDPN QPFYLVAPDE LQKDYLSPFS LPSKLVFLTK
860 870 880 890 900
TFPRLRVIWS RSYYCTTKIY DQIKDGYPEP DPSMVNVIPE VNDDQNYNFN
910 920 930 940 950
AQDVLRTMPG VNDKNINLIM DNVDDLYHLS KLSLSEFSTI MNDSVNNNKN
960
ATLLFNFFNN QLNQ
Length:964
Mass (Da):110,646
Last modified:May 24, 2005 - 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:iDF43358D74CEF98B
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
AAFI02000064 Genomic DNA Translation: EAL65258.1

NCBI Reference Sequences

More...
RefSeqi
XP_638619.1, XM_633527.1

Genome annotation databases

Ensembl protists genome annotation project

More...
EnsemblProtistsi
EAL65258; EAL65258; DDB_G0284419

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
8624590

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ddi:DDB_G0284419

<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
AAFI02000064 Genomic DNA Translation: EAL65258.1
RefSeqiXP_638619.1, XM_633527.1

3D structure databases

SMRiQ54PN5
ModBaseiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0232364

Proteomic databases

PaxDbiQ54PN5

Genome annotation databases

EnsemblProtistsiEAL65258; EAL65258; DDB_G0284419
GeneIDi8624590
KEGGiddi:DDB_G0284419

Organism-specific databases

dictyBaseiDDB_G0284419, xpf

Phylogenomic databases

eggNOGiKOG0442, Eukaryota
HOGENOMiCLU_002265_2_0_1
InParanoidiQ54PN5
OMAiFHKILQA
PhylomeDBiQ54PN5

Enzyme and pathway databases

ReactomeiR-DDI-5696395, Formation of Incision Complex in GG-NER
R-DDI-6782135, Dual incision in TC-NER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q54PN5

Family and domain databases

InterProiView protein in InterPro
IPR006166, ERCC4_domain
IPR011335, Restrct_endonuc-II-like
IPR010994, RuvA_2-like
PfamiView protein in Pfam
PF02732, ERCC4, 1 hit
SMARTiView protein in SMART
SM00891, ERCC4, 1 hit
SUPFAMiSSF47781, SSF47781, 1 hit
SSF52980, SSF52980, 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 nameiXPF_DICDI
<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: Q54PN5
<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: April 29, 2008
Last sequence update: May 24, 2005
Last modified: December 2, 2020
This is version 98 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)

<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. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. SIMILARITY comments
    Index of protein domains and families
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