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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-Experimental evidence at transcript leveli

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

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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi30 – 301Magnesium 1By similarity
Metal bindingi77 – 771Magnesium 1By similarity
Metal bindingi777 – 7771Magnesium 1By similarity
Metal bindingi779 – 7791Magnesium 1By similarity
Metal bindingi798 – 7981Magnesium 2By similarity
Metal bindingi800 – 8001Magnesium 2By similarity
Metal bindingi849 – 8491Magnesium 2By similarity

GO - Molecular functioni

GO - Biological processi

  • nucleotide-excision repair Source: PomBase
  • nucleotide-excision repair, DNA incision, 3'-to lesion Source: PomBase
  • nucleotide-excision repair involved in interstrand cross-link repair Source: PomBase
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

ReactomeiR-SPO-5696400. Dual Incision in GG-NER.
R-SPO-6782135. Dual incision in TC-NER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA repair protein rad13 (EC:3.1.-.-)
Gene namesi
Name:rad13
ORF Names:SPBC3E7.08c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC3E7.08c.
PomBaseiSPBC3E7.08c. rad13.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11121112DNA repair protein rad13PRO_0000154036Add
BLAST

Proteomic databases

MaxQBiP28706.

Interactioni

Protein-protein interaction databases

BioGridi277566. 70 interactions.
MINTiMINT-4688067.

Structurei

3D structure databases

ProteinModelPortaliP28706.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini395 – 41420UIMPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 9595N-domainAdd
BLAST
Regioni742 – 870129I-domainAdd
BLAST

Sequence similaritiesi

Contains 1 UIM (ubiquitin-interacting motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

HOGENOMiHOG000214817.
InParanoidiP28706.
KOiK10846.
OMAiFQATMRD.
OrthoDBiEOG7QK0MK.
PhylomeDBiP28706.

Family and domain databases

Gene3Di3.40.50.1010. 2 hits.
InterProiIPR020045. 5-3_exonuclease_C.
IPR008918. HhH2.
IPR029060. PIN_domain-like.
IPR003903. UIM_dom.
IPR006086. XPG-I_dom.
IPR006084. XPG/Rad2.
IPR001044. XPG/Rad2_eukaryotes.
IPR019974. XPG_CS.
IPR006085. XPG_DNA_repair_N.
[Graphical view]
PfamiPF00867. XPG_I. 1 hit.
PF00752. XPG_N. 1 hit.
[Graphical view]
PRINTSiPR00853. XPGRADSUPER.
PR00066. XRODRMPGMNTG.
SMARTiSM00279. HhH2. 1 hit.
SM00484. XPGI. 1 hit.
SM00485. XPGN. 1 hit.
[Graphical view]
SUPFAMiSSF47807. SSF47807. 2 hits.
SSF88723. SSF88723. 2 hits.
TIGRFAMsiTIGR00600. rad2. 1 hit.
PROSITEiPS50330. UIM. 1 hit.
PS00841. XPG_1. 1 hit.
PS00842. XPG_2. 1 hit.
[Graphical view]

Sequencei

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
Checksum:i7ECF4229D5BF4768
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti8 – 81D → N in CAA47291 (PubMed:8464724).Curated
Sequence conflicti738 – 7436LKNQKR → AQKSKKG in CAA47291 (PubMed:8464724).Curated

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.

Genome annotation databases

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

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

ProteinModelPortaliP28706.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277566. 70 interactions.
MINTiMINT-4688067.

Proteomic databases

MaxQBiP28706.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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

HOGENOMiHOG000214817.
InParanoidiP28706.
KOiK10846.
OMAiFQATMRD.
OrthoDBiEOG7QK0MK.
PhylomeDBiP28706.

Enzyme and pathway databases

ReactomeiR-SPO-5696400. Dual Incision in GG-NER.
R-SPO-6782135. Dual incision in TC-NER.

Miscellaneous databases

PROiP28706.

Family and domain databases

Gene3Di3.40.50.1010. 2 hits.
InterProiIPR020045. 5-3_exonuclease_C.
IPR008918. HhH2.
IPR029060. PIN_domain-like.
IPR003903. UIM_dom.
IPR006086. XPG-I_dom.
IPR006084. XPG/Rad2.
IPR001044. XPG/Rad2_eukaryotes.
IPR019974. XPG_CS.
IPR006085. XPG_DNA_repair_N.
[Graphical view]
PfamiPF00867. XPG_I. 1 hit.
PF00752. XPG_N. 1 hit.
[Graphical view]
PRINTSiPR00853. XPGRADSUPER.
PR00066. XRODRMPGMNTG.
SMARTiSM00279. HhH2. 1 hit.
SM00484. XPGI. 1 hit.
SM00485. XPGN. 1 hit.
[Graphical view]
SUPFAMiSSF47807. SSF47807. 2 hits.
SSF88723. SSF88723. 2 hits.
TIGRFAMsiTIGR00600. rad2. 1 hit.
PROSITEiPS50330. UIM. 1 hit.
PS00841. XPG_1. 1 hit.
PS00842. XPG_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Evolutionary conservation of excision repair in Schizosaccharomyces pombe: evidence for a family of sequences related to the Saccharomyces cerevisiae RAD2 gene."
    Carr A.M., Sheldrick K.S., Murray J.M., Al-Harithy R., Watts F.Z., Lehmann A.R.
    Nucleic Acids Res. 21:1345-1349(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.

Entry informationi

Entry nameiRAD13_SCHPO
AccessioniPrimary (citable) accession number: P28706
Secondary accession number(s): O59728
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: February 21, 2001
Last modified: June 8, 2016
This is version 126 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  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.