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Protein

DNA repair endonuclease XPF

Gene

Ercc4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Catalytic component of a 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

Cofactori

Mg2+By similarity

GO - Molecular functioni

  1. damaged DNA binding Source: MGI
  2. endodeoxyribonuclease activity Source: MGI
  3. protein C-terminus binding Source: MGI
  4. protein N-terminus binding Source: MGI
  5. single-stranded DNA binding Source: MGI
  6. single-stranded DNA endodeoxyribonuclease activity Source: GO_Central
  7. TFIID-class transcription factor binding Source: MGI

GO - Biological processi

  1. DNA catabolic process, endonucleolytic Source: MGI
  2. DNA repair Source: MGI
  3. double-strand break repair via homologous recombination Source: MGI
  4. negative regulation of telomere maintenance Source: MGI
  5. nucleotide-excision repair Source: MGI
  6. nucleotide-excision repair, DNA incision Source: MGI
  7. nucleotide-excision repair, DNA incision, 3'-to lesion Source: MGI
  8. nucleotide-excision repair, DNA incision, 5'-to lesion Source: MGI
  9. nucleotide-excision repair involved in interstrand cross-link repair Source: GO_Central
  10. resolution of meiotic recombination intermediates Source: GO_Central
  11. response to UV Source: MGI
  12. telomere maintenance Source: MGI
  13. telomere maintenance via telomere shortening Source: MGI
  14. UV protection Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding, Magnesium

Enzyme and pathway databases

ReactomeiREACT_279019. Dual incision reaction in TC-NER.
REACT_296832. Dual incision reaction in GG-NER.
REACT_302527. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_314261. Formation of incision complex in GG-NER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA repair endonuclease XPF (EC:3.1.-.-)
Alternative name(s):
DNA excision repair protein ERCC-4
Gene namesi
Name:Ercc4
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 16

Organism-specific databases

MGIiMGI:1354163. Ercc4.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. chromosome, telomeric region Source: MGI
  2. nuclear chromosome, telomeric region Source: MGI
  3. nucleotide-excision repair complex Source: MGI
  4. nucleotide-excision repair factor 1 complex Source: MGI
  5. nucleus Source: MGI
  6. transcription factor TFIID complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 917917DNA repair endonuclease XPFPRO_0000198854Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei289 – 2891N6-acetyllysineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ9QZD4.
PaxDbiQ9QZD4.
PRIDEiQ9QZD4.

PTM databases

PhosphoSiteiQ9QZD4.

Expressioni

Gene expression databases

BgeeiQ9QZD4.
ExpressionAtlasiQ9QZD4. baseline and differential.
GenevestigatoriQ9QZD4.

Interactioni

Subunit structurei

Heterodimer composed of ERCC1 and XPF/ERCC4. Interacts with SLX4/BTBD12; this interaction is direct and links the ERCC1-XPF/ERCC1 complex to SLX4, which may coordinate the action of the structure-specific endonuclease during DNA repair (By similarity).By similarity

Structurei

3D structure databases

ProteinModelPortaliQ9QZD4.
SMRiQ9QZD4. Positions 677-819, 835-917.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini684 – 76481ERCC4Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 457457Helicase-likeBy similarityAdd
BLAST
Regioni233 – 25422Leucine-zipper 1Add
BLAST
Regioni270 – 29829Leucine-zipper 2Add
BLAST
Regioni659 – 814156NucleaseBy similarityAdd
BLAST
Regioni838 – 90669HhH2, dimerization with ERCC1By similarityAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi487 – 4926Nuclear localization signalSequence Analysis

Sequence similaritiesi

Belongs to the XPF family.Curated
Contains 1 ERCC4 domain.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1948.
GeneTreeiENSGT00390000004394.
HOGENOMiHOG000202204.
HOVERGENiHBG051500.
InParanoidiQ9QZD4.
KOiK10848.
OMAiQQSIVVD.
OrthoDBiEOG7VTDM8.
PhylomeDBiQ9QZD4.
TreeFamiTF101234.

Family and domain databases

Gene3Di3.40.50.10130. 1 hit.
InterProiIPR020819. DNA_repair_nuc_XPF/helicase.
IPR006166. ERCC4_domain.
IPR006167. Rad1.
IPR011335. Restrct_endonuc-II-like.
IPR010994. RuvA_2-like.
[Graphical view]
PfamiPF02732. ERCC4. 1 hit.
[Graphical view]
SMARTiSM00891. ERCC4. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF52980. SSF52980. 1 hit.
TIGRFAMsiTIGR00596. rad1. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9QZD4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEPGLSGERR SMAPLLEYER QQVLELLDSD GLVVCARGLG TDRLLYHFLR
60 70 80 90 100
LHCHPACLVL VLNTQPAEEE YFINQLKIEG VEHLPRRVTN EIASNSRYEV
110 120 130 140 150
YTQGGIIFAT SRILVVDFLT GRIPSDLITG ILVYRAHRII ESCQEAFILR
160 170 180 190 200
LFRQKNKRGF IKAFTDNAVA FDTGFCHVER VMRNLFVRKL YLWPRFHVAV
210 220 230 240 250
NSFLEQHKPE VVEIHVSMTP AMLAIQTAIL DILNACLKEL KCHNPSLEVE
260 270 280 290 300
DLSLENALGK PFDKTIRHYL DPLWHQLGAK TKSLVQDLKI LRTLLQYLSQ
310 320 330 340 350
YDCVTFLNLL ESLRATEKVF GQNSGWLFLD ASTSMFVNAR ARVYRVPDVK
360 370 380 390 400
LNKKAKTSEK TSSPEVQETK KELVLESNPK WEALTDVLKE IEAENKESEA
410 420 430 440 450
LGGPGRVLIC ASDDRTCCQL RDYLSAGAET FLLRLYRKTF EKDGKAEEVW
460 470 480 490 500
VNVRKGDGPK RTTKSDKRPK AAPNKERASA KRGAPLKRKK QELTLTQVLG
510 520 530 540 550
SAEEPPEDKA LEEDLCRQTS SSPEGCGVEI KRESFDLNVS SDAAYGILKE
560 570 580 590 600
PLTIIHPLLG CSDPYALTRV LHEVEPRYVV LYDAELTFVR QLEIYRASRP
610 620 630 640 650
GKPLRVYFLI YGGSTEEQRY LTALRKEKEA FEKLIREKAS MVVPEEREGR
660 670 680 690 700
DETNLDLARG SAALDAPTDT RKAGGQEQNG TQSSIVVDMR EFRSELPSLI
710 720 730 740 750
HRRGIDIEPV TLEVGDYILT PELCVERKSV SDLIGSLHSG RLYSQCLAMS
760 770 780 790 800
RYYRRPVLLI EFDPSKPFSL APRGAFFQEM SSSDVSSKLT LLTLHFPRLR
810 820 830 840 850
LLWCPSPHAT AELFEELKQN KPQPDAATAM AITADSETLP ESDRYNPGPQ
860 870 880 890 900
DFVLKMPGVN AKNCRSLMNQ VKNIAELATL SLERLTTILG HSGNAKQLHD
910
FLHTAYADLV SKGRVRK
Length:917
Mass (Da):103,690
Last modified:May 5, 2009 - v3
Checksum:i2206DC264BC4E233
GO

Sequence cautioni

The sequence AAH26792.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti30 – 301D → N in AAF03157 (PubMed:10644440).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF189285 mRNA. Translation: AAF03157.1.
AC004155 Genomic DNA. Translation: AAC03240.1.
BC026792 mRNA. Translation: AAH26792.1. Different initiation.
CCDSiCCDS37256.1.
RefSeqiNP_056584.2. NM_015769.2.
UniGeneiMm.287837.

Genome annotation databases

EnsembliENSMUST00000023206; ENSMUSP00000023206; ENSMUSG00000022545.
GeneIDi50505.
KEGGimmu:50505.
UCSCiuc007yfx.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF189285 mRNA. Translation: AAF03157.1.
AC004155 Genomic DNA. Translation: AAC03240.1.
BC026792 mRNA. Translation: AAH26792.1. Different initiation.
CCDSiCCDS37256.1.
RefSeqiNP_056584.2. NM_015769.2.
UniGeneiMm.287837.

3D structure databases

ProteinModelPortaliQ9QZD4.
SMRiQ9QZD4. Positions 677-819, 835-917.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

PhosphoSiteiQ9QZD4.

Proteomic databases

MaxQBiQ9QZD4.
PaxDbiQ9QZD4.
PRIDEiQ9QZD4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000023206; ENSMUSP00000023206; ENSMUSG00000022545.
GeneIDi50505.
KEGGimmu:50505.
UCSCiuc007yfx.2. mouse.

Organism-specific databases

CTDi2072.
MGIiMGI:1354163. Ercc4.

Phylogenomic databases

eggNOGiCOG1948.
GeneTreeiENSGT00390000004394.
HOGENOMiHOG000202204.
HOVERGENiHBG051500.
InParanoidiQ9QZD4.
KOiK10848.
OMAiQQSIVVD.
OrthoDBiEOG7VTDM8.
PhylomeDBiQ9QZD4.
TreeFamiTF101234.

Enzyme and pathway databases

ReactomeiREACT_279019. Dual incision reaction in TC-NER.
REACT_296832. Dual incision reaction in GG-NER.
REACT_302527. Formation of transcription-coupled NER (TC-NER) repair complex.
REACT_314261. Formation of incision complex in GG-NER.

Miscellaneous databases

NextBioi307508.
PROiQ9QZD4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9QZD4.
ExpressionAtlasiQ9QZD4. baseline and differential.
GenevestigatoriQ9QZD4.

Family and domain databases

Gene3Di3.40.50.10130. 1 hit.
InterProiIPR020819. DNA_repair_nuc_XPF/helicase.
IPR006166. ERCC4_domain.
IPR006167. Rad1.
IPR011335. Restrct_endonuc-II-like.
IPR010994. RuvA_2-like.
[Graphical view]
PfamiPF02732. ERCC4. 1 hit.
[Graphical view]
SMARTiSM00891. ERCC4. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF52980. SSF52980. 1 hit.
TIGRFAMsiTIGR00596. rad1. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of the mouse xpf DNA repair gene and differential expression during spermatogenesis."
    Shannon M., Lamerdin J.E., Richardson L., McCutchen-Maloney S.L., Hwang M.H., Handel M.A., Stubbs L., Thelen M.P.
    Genomics 62:427-435(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 5-917.
    Tissue: Salivary gland.

Entry informationi

Entry nameiXPF_MOUSE
AccessioniPrimary (citable) accession number: Q9QZD4
Secondary accession number(s): O54810, Q8R0I3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 13, 2004
Last sequence update: May 5, 2009
Last modified: April 1, 2015
This is version 113 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.