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UniProtKB - P28706 (RAD13_SCHPO)

Entry version 147 (17 Jun 2020)
Sequence version 2 (21 Feb 2001)
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Protein

DNA repair protein rad13

Gene

rad13

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
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>-Experimental evidence at transcript 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

Single-stranded DNA endonuclease involved in excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Essential for the incision step of excision-repair (Probable).Curated

<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 similarityNote: Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi30Magnesium 1By similarity1
Metal bindingi77Magnesium 1By similarity1
Metal bindingi777Magnesium 1By similarity1
Metal bindingi779Magnesium 1By similarity1
Metal bindingi798Magnesium 2By similarity1
Metal bindingi800Magnesium 2By similarity1
Metal bindingi849Magnesium 2By similarity1

<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

Molecular functionEndonuclease, Hydrolase, Nuclease
Biological processDNA damage, DNA repair
LigandMagnesium, Metal-binding

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-SPO-5696395 Formation of Incision Complex in GG-NER
R-SPO-5696400 Dual Incision in GG-NER
R-SPO-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 protein rad13 (EC:3.1.-.-)
<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:rad13
ORF Names:SPBC3E7.08c
<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>OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission 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 identifieri284812 [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 › Taphrinomycotina › Schizosaccharomycetes › Schizosaccharomycetales › Schizosaccharomycetaceae › Schizosaccharomyces ›
<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
  • UP000002485 <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 II

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...EuPathDBi		FungiDB:SPBC3E7.08c

Schizosaccharomyces pombe database

More...PomBasei		SPBC3E7.08c rad13

<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

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_00001540361 – 1112DNA repair protein rad13Add BLAST1112

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		P28706

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

More...PaxDbi		P28706

PRoteomics IDEntifications database

More...PRIDEi		P28706

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		P28706

<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

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		277566, 74 interactors

STRING: functional protein association networks

More...STRINGi		4896.SPBC3E7.08c.1

<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		P28706

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>Domaini395 – 414UIMPROSITE-ProRule annotationAdd BLAST20

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 95N-domainAdd BLAST95
Regioni742 – 870I-domainAdd BLAST129

<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 XPG/RAD2 endonuclease family. XPG subfamily.Curated

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_003018_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P28706

KEGG Orthology (KO)

More...KOi		K10846

Identification of Orthologs from Complete Genome Data

More...OMAi		RNRQDRM

Database for complete collections of gene phylogenies

More...PhylomeDBi		P28706

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR036279 5-3_exonuclease_C_sf
IPR008918 HhH2
IPR029060 PIN-like_dom_sf
IPR003903 UIM_dom
IPR006086 XPG-I_dom
IPR006084 XPG/Rad2
IPR001044 XPG/Rad2_eukaryotes
IPR019974 XPG_CS
IPR006085 XPG_DNA_repair_N

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00867 XPG_I, 1 hit
PF00752 XPG_N, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00853 XPGRADSUPER
PR00066 XRODRMPGMNTG

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00279 HhH2, 1 hit
SM00484 XPGI, 1 hit
SM00485 XPGN, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF47807 SSF47807, 1 hit
SSF88723 SSF88723, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00600 rad2, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50330 UIM, 1 hit
PS00841 XPG_1, 1 hit
PS00842 XPG_2, 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.

P28706-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MGVSGLWDIL EPVKRPVKLE TLVNKRLAID ASIWIYQFLK AVRDKEGNQL 
        60         70         80         90        100
KSSHVVGFFR RICKLLFFGI KPVFVFDGGA PSLKRQTIQK RQARRLDREE 
       110        120        130        140        150
NATVTANKLL ALQMRHQAML LEENNKKATA LANASVQNER QMPSSMTLDN 
       160        170        180        190        200
SEIKPVLNQR KNYLKPDPYQ LPEMDVSFDK LGSSYDPRIM SQDELTQYVS 
       210        220        230        240        250
SFTKIEDINL FDFSNIDFDS ELFQSLPDTD KYSILSAARL RSRLRMGLSS 
       260        270        280        290        300
EQLSEMFPNR MDFSRFQIER LKERNDLTQR LMDFTGMNEF GPSRVVSEKN 
       310        320        330        340        350
REYILVKNEG AEGGWALGVI SGSTNNEPII IDDEATKLSS NLIDEDEDEA 
       360        370        380        390        400
FYDVPLPSRS HSMNPRELVA AKLKEIKENS FSENQQSDEA DYNVTDDLIL 
       410        420        430        440        450
QLATQQSLEE NKKSKELFSL SASEFDKLNS EKKTFEILST DIPAEDSMNS 
       460        470        480        490        500
LLNDEENLKL EHVGDVSNDS LAFAEKKHPE NGTSIFMDAL PSASREKKTN 
       510        520        530        540        550
DLIDPLPFQP MDWGKSIFFE KLKKPTETFM DSKTDIPSEA PDNSKLVEDT 
       560        570        580        590        600
NLHTINATVN IESDLDAAKP GIENPIISPL LPVKDDEKDL DLRELNPLEP 
       610        620        630        640        650
FENMKEQADD GTVTNPLNVS SDKAMSVYLL SSENAKDTGD IKSESIDAVL 
       660        670        680        690        700
PTLETSSPSL SIPTDFQKEA SPNKGAAALS SKVEPEVVEK LLDEEEEEMI 
       710        720        730        740        750
IRMAEEEKEY DRFVSELNQR HETEEWNQEA FEKRLKELKN QKRSEKRDAD 
       760        770        780        790        800
EVTQVMIKEC QELLRLFGLP YIVAPQEAEA QCSKLLELKL VDGIVTDDSD 
       810        820        830        840        850
VFLFGGTRVY RNMFNQNKFV ELYLMDDMKR EFNVNQMDLI KLAHLLGSDY 
       860        870        880        890        900
TMGLSRVGPV LALEILHEFP GDTGLFEFKK WFQRLSTGHA SKNDVNTPVK 
       910        920        930        940        950
KRINKLVGKI ILPSEFPNPL VDEAYLHPAV DDSKQSFQWG IPDLDELRQF 
       960        970        980        990       1000
LMATVGWSKQ RTNEVLLPVI QDMHKKQFVG TQSNLTQFFE GGNTNVYAPR 
      1010       1020       1030       1040       1050
VAYHFKSKRL ENALSSFKNQ ISNQSPMSEE IQADADAFGE SKGSDELQSR 
      1060       1070       1080       1090       1100
ILRRKKMMAS KNSSDSDSDS EDNFLASLTP KTNSSSISIE NLPRKTKLST 
      1110 
SLLKKPSKRR RK
Length:1,112
Mass (Da):126,329
Last modified:February 21, 2001 - v2
<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:i7ECF4229D5BF4768
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti8D → N in CAA47291 (PubMed:8464724).Curated1
Sequence conflicti738 – 743LKNQKR → AQKSKKG in CAA47291 (PubMed:8464724).Curated6

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
X66795 mRNA Translation: CAA47291.1
CU329671 Genomic DNA Translation: CAA19011.1

Protein sequence database of the Protein Information Resource

More...PIRi		S30301
T40382

NCBI Reference Sequences

More...RefSeqi		NP_596095.1, NM_001022011.2

Genome annotation databases

Ensembl fungal genome annotation project

More...EnsemblFungii		SPBC3E7.08c.1; SPBC3E7.08c.1:pep; SPBC3E7.08c

Database of genes from NCBI RefSeq genomes

More...GeneIDi		2541051

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		spo:SPBC3E7.08c

<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
X66795 mRNA Translation: CAA47291.1
CU329671 Genomic DNA Translation: CAA19011.1
PIRiS30301
T40382
RefSeqiNP_596095.1, NM_001022011.2

3D structure databases

SMRiP28706
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi277566, 74 interactors
STRINGi4896.SPBC3E7.08c.1

PTM databases

iPTMnetiP28706

Proteomic databases

MaxQBiP28706
PaxDbiP28706
PRIDEiP28706

Genome annotation databases

EnsemblFungiiSPBC3E7.08c.1; SPBC3E7.08c.1:pep; SPBC3E7.08c
GeneIDi2541051
KEGGispo:SPBC3E7.08c

Organism-specific databases

EuPathDBiFungiDB:SPBC3E7.08c
PomBaseiSPBC3E7.08c rad13

Phylogenomic databases

HOGENOMiCLU_003018_0_0_1
InParanoidiP28706
KOiK10846
OMAiRNRQDRM
PhylomeDBiP28706

Enzyme and pathway databases

ReactomeiR-SPO-5696395 Formation of Incision Complex in GG-NER
R-SPO-5696400 Dual Incision in GG-NER
R-SPO-6782135 Dual incision in TC-NER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P28706

Family and domain databases

InterProiView protein in InterPro
IPR036279 5-3_exonuclease_C_sf
IPR008918 HhH2
IPR029060 PIN-like_dom_sf
IPR003903 UIM_dom
IPR006086 XPG-I_dom
IPR006084 XPG/Rad2
IPR001044 XPG/Rad2_eukaryotes
IPR019974 XPG_CS
IPR006085 XPG_DNA_repair_N
PfamiView protein in Pfam
PF00867 XPG_I, 1 hit
PF00752 XPG_N, 1 hit
PRINTSiPR00853 XPGRADSUPER
PR00066 XRODRMPGMNTG
SMARTiView protein in SMART
SM00279 HhH2, 1 hit
SM00484 XPGI, 1 hit
SM00485 XPGN, 1 hit
SUPFAMiSSF47807 SSF47807, 1 hit
SSF88723 SSF88723, 1 hit
TIGRFAMsiTIGR00600 rad2, 1 hit
PROSITEiView protein in PROSITE
PS50330 UIM, 1 hit
PS00841 XPG_1, 1 hit
PS00842 XPG_2, 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 nameiRAD13_SCHPO
<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: P28706
Secondary accession number(s): O59728
<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: December 1, 1992
Last sequence update: February 21, 2001
Last modified: June 17, 2020
This is version 147 of the entry and version 2 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. SIMILARITY comments
    Index of protein domains and families
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
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