Q92889 (XPF_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
May 1, 2013.
Version 139.
History...
Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: DNA repair endonuclease XPF EC=3.1.-.- Alternative name(s): DNA excision repair protein ERCC-4 DNA repair protein complementing XP-F cells Xeroderma pigmentosum group F-complementing protein | ||||
| Gene names |
| ||||
| Organism | Homo sapiens (Human) [Reference proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo![]() |
Protein attributes
| Sequence length | 916 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence at protein level |
General annotation (Comments)
| Function | 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. Ref.7 |
| Cofactor | Magnesium. |
| Subunit structure | Heterodimer composed of ERCC1 and XPF/ERCC4. Interacts with EME1. 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. Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 |
| Subcellular location | Nucleus Probable. |
| Involvement in disease | Xeroderma pigmentosum complementation group F (XP-F) [MIM:278760]: An autosomal recessive pigmentary skin disorder characterized by solar hypersensitivity of the skin, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities. The skin develops marked freckling and other pigmentation abnormalities. XP-F patients show a mild phenotype. XFE progeroid syndrome (XFEPS) [MIM:610965]: A syndrome characterized by aged bird-like facies, lack of subcutaneous fat, dwarfism, cachexia and microcephaly. Additional features include sun-sensitivity from birth, learning disabilities, hearing loss, and visual impairment. |
| Sequence similarities | Belongs to the XPF family. Contains 1 ERCC4 domain. |
| Sequence caution | The sequence AAB07689.1 differs from that shown. Reason: Erroneous initiation. |
Ontologies
Binary interactions
With | Entry | #Exp. | IntAct | Notes |
|---|---|---|---|---|
| SLX4 | Q8IY92 | 10 | EBI-2370770,EBI-2370740 |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||||||||||||||||||
Molecule processing | |||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 916 | 916 | DNA repair endonuclease XPF | PRO_0000198853 | |||||||||||||||||||||||
Regions | |||||||||||||||||||||||||||
| Domain | 683 – 763 | 81 | ERCC4 | ||||||||||||||||||||||||
| Region | 233 – 254 | 22 | Leucine-zipper 1 | ||||||||||||||||||||||||
| Region | 270 – 298 | 29 | Leucine-zipper 2 | ||||||||||||||||||||||||
| Region | 617 – 916 | 300 | Interaction with EME1 and ERCC1 | ||||||||||||||||||||||||
| Motif | 486 – 491 | 6 | Nuclear localization signal Potential | ||||||||||||||||||||||||
Amino acid modifications | |||||||||||||||||||||||||||
| Modified residue | 289 | 1 | N6-acetyllysine Ref.11 | ||||||||||||||||||||||||
Natural variations | |||||||||||||||||||||||||||
| Natural variant | 33 | 1 | V → L. Corresponds to variant rs34205098 [ dbSNP | Ensembl ]. | VAR_057477 | |||||||||||||||||||||||
| Natural variant | 153 | 1 | R → P in XFEPS. Ref.17 | VAR_034802 | |||||||||||||||||||||||
| Natural variant | 168 | 1 | A → V. Ref.3 Corresponds to variant rs2020961 [ dbSNP | Ensembl ]. | VAR_014769 | |||||||||||||||||||||||
| Natural variant | 225 | 1 | I → M in XP-F. Ref.14 | VAR_008200 | |||||||||||||||||||||||
| Natural variant | 379 | 1 | P → S. Ref.3 Ref.13 Corresponds to variant rs1799802 [ dbSNP | Ensembl ]. | VAR_013395 | |||||||||||||||||||||||
| Natural variant | 415 | 1 | R → Q. Ref.2 Ref.3 Ref.16 Corresponds to variant rs1800067 [ dbSNP | Ensembl ]. | VAR_013396 | |||||||||||||||||||||||
| Natural variant | 454 | 1 | R → W in XP-F. Ref.14 | VAR_008201 | |||||||||||||||||||||||
| Natural variant | 490 | 1 | R → Q in XP-F. Ref.14 | VAR_008202 | |||||||||||||||||||||||
| Natural variant | 502 | 1 | E → K in XP-F. Ref.14 | VAR_008203 | |||||||||||||||||||||||
| Natural variant | 513 | 1 | G → R in XP-F. Ref.14 | VAR_008204 | |||||||||||||||||||||||
| Natural variant | 529 | 1 | I → T in XP-F. Ref.14 | VAR_008205 | |||||||||||||||||||||||
| Natural variant | 567 | 1 | T → A in XP-F. Ref.14 | VAR_008206 | |||||||||||||||||||||||
| Natural variant | 576 | 1 | R → T. Ref.16 Corresponds to variant rs1800068 [ dbSNP | Ensembl ]. | VAR_013397 | |||||||||||||||||||||||
| Natural variant | 605 – 611 | 7 | Missing in XP-F. | VAR_008207 | |||||||||||||||||||||||
| Natural variant | 608 | 1 | L → P in XP-F. Ref.14 | VAR_013398 | |||||||||||||||||||||||
| Natural variant | 662 | 1 | S → P. Ref.3 Corresponds to variant rs2020955 [ dbSNP | Ensembl ]. | VAR_014770 | |||||||||||||||||||||||
| Natural variant | 703 | 1 | G → D. Ref.4 | VAR_005849 | |||||||||||||||||||||||
| Natural variant | 706 | 1 | I → T. Ref.3 Corresponds to variant rs1800069 [ dbSNP | Ensembl ]. | VAR_014771 | |||||||||||||||||||||||
| Natural variant | 717 | 1 | I → T. Ref.16 | VAR_013399 | |||||||||||||||||||||||
| Natural variant | 768 | 1 | S → F. Corresponds to variant rs12928650 [ dbSNP | Ensembl ]. | VAR_057478 | |||||||||||||||||||||||
| Natural variant | 799 | 1 | R → W in XP-F; mild; significant residual repair activity. Ref.4 Ref.15 | VAR_005850 | |||||||||||||||||||||||
| Natural variant | 860 | 1 | A → D. Corresponds to variant rs4986933 [ dbSNP | Ensembl ]. | VAR_057479 | |||||||||||||||||||||||
| Natural variant | 873 | 1 | I → V. Ref.3 Corresponds to variant rs2020957 [ dbSNP | Ensembl ]. | VAR_019201 | |||||||||||||||||||||||
| Natural variant | 875 | 1 | E → G. Ref.3 Ref.16 Corresponds to variant rs1800124 [ dbSNP | Ensembl ]. | VAR_013408 | |||||||||||||||||||||||
| Natural variant | 912 | 1 | G → E. Corresponds to variant rs2020956 [ dbSNP | Ensembl ]. | VAR_014772 | |||||||||||||||||||||||
Secondary structure | |||||||||||||||||||||||||||
Helix Strand Turn | |||||||||||||||||||||||||||
| Turn | 835 – 837 | 3 | |||||||||||||||||||||||||
| Helix | 839 – 842 | 4 | |||||||||||||||||||||||||
| Helix | 850 – 853 | 4 | |||||||||||||||||||||||||
| Helix | 860 – 869 | 10 | |||||||||||||||||||||||||
| Beta strand | 870 – 872 | 3 | |||||||||||||||||||||||||
| Helix | 873 – 877 | 5 | |||||||||||||||||||||||||
| Helix | 881 – 888 | 8 | |||||||||||||||||||||||||
| Helix | 891 – 902 | 12 | |||||||||||||||||||||||||
| Helix | 905 – 908 | 4 | |||||||||||||||||||||||||
| Beta strand | 911 – 913 | 3 | |||||||||||||||||||||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "ERCC4 (XPF) encodes a human nucleotide excision repair protein with eukaryotic recombination homologs." Brookman K.W., Lamerdin J.E., Thelen M.P., Hwang M., Reardon J.T., Sancar A., Zhou Z.-Q., Walter C.A., Parris C.N., Thompson L.H. Mol. Cell. Biol. 16:6553-6562(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. |
| [2] | "Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. Sugano S.Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT GLN-415. Tissue: Brain. |
| [3] | NIEHS SNPs program Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS VAL-168; SER-379; GLN-415; PRO-662; THR-706; VAL-873 AND GLY-875. |
| [4] | "Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease." Sijbers A.M., de Laat W.L., Ariza R.R., Biggerstaff M., Wei Y.-F., Moggs J.G., Carter K.C., Shell B.K., Evans E., de Jong M.C., Rademakers S., de Rooij J., Jaspers N.G.J., Hoeijmakers J.H.J., Wood R.D. Cell 86:811-822(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 7-916, VARIANT ASP-703, VARIANT XP-F TRP-799. Tissue: Fibroblast. |
| [5] | "A summary of mutations in the UV-sensitive disorders: xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy." Cleaver J.E., Thompson L.H., Richardson A.S., States J.C. Hum. Mutat. 14:9-22(1999) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW ON VARIANTS XP-F. |
| [6] | "Identification of FAAP24, a Fanconi anemia core complex protein that interacts with FANCM." Ciccia A., Ling C., Coulthard R., Yan Z., Xue Y., Meetei A.R., Laghmani el H., Joenje H., McDonald N., de Winter J.P., Wang W., West S.C. Mol. Cell 25:331-343(2007) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH EME1 AND ERCC1. |
| [7] | "Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair." Svendsen J.M., Smogorzewska A., Sowa M.E., O'Connell B.C., Gygi S.P., Elledge S.J., Harper J.W. Cell 138:63-77(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH SLX4. |
| [8] | "Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases." Fekairi S., Scaglione S., Chahwan C., Taylor E.R., Tissier A., Coulon S., Dong M.-Q., Ruse C., Yates J.R. III, Russell P., Fuchs R.P., McGowan C.H., Gaillard P.-H.L. Cell 138:78-89(2009) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH SLX4. |
| [9] | "Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair." Munoz I.M., Hain K., Declais A.-C., Gardiner M., Toh G.W., Sanchez-Pulido L., Heuckmann J.M., Toth R., Macartney T., Eppink B., Kanaar R., Ponting C.P., Lilley D.M.J., Rouse J. Mol. Cell 35:116-127(2009) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH SLX4. |
| [10] | "Drosophila MUS312 and the vertebrate ortholog BTBD12 interact with DNA structure-specific endonucleases in DNA repair and recombination." Andersen S.L., Bergstralh D.T., Kohl K.P., LaRocque J.R., Moore C.B., Sekelsky J. Mol. Cell 35:128-135(2009) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH SLX4. |
| [11] | "Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-289, MASS SPECTROMETRY. |
| [12] | "Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. |
| [13] | "Nonconservative amino acid substitution variants exist at polymorphic frequency in DNA repair genes in healthy humans." Shen M.R., Jones I.M., Mohrenweiser H. Cancer Res. 58:604-608(1998) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT SER-379. |
| [14] | "Characterization of molecular defects in Xeroderma pigmentosum group F in relation to its clinically mild symptoms." Matsumura Y., Nishigori C., Yagi T., Imamura S., Takebe H. Hum. Mol. Genet. 7:969-974(1998) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS XP-F MET-225; TRP-454; GLN-490; LYS-502; ARG-513; THR-529; ALA-567; 605-VAL--GLY-611 DEL AND PRO-608. |
| [15] | "Homozygous R788W point mutation in the XPF gene of a patient with xeroderma pigmentosum and late-onset neurologic disease." Sijbers A.M., van Voorst Vader P.C., Snoek J.W., Raams A., Jaspers N.G.J., Kleijer W.J. J. Invest. Dermatol. 110:832-836(1998) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT XP-F TRP-799. |
| [16] | "Polymorphisms in the human DNA repair gene XPF." Fan F., Liu C., Tavare S., Arnheim N. Mutat. Res. 406:115-120(1999) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS GLN-415; THR-576; THR-717 AND GLY-875. |
| [17] | "A new progeroid syndrome reveals that genotoxic stress suppresses the somatotroph axis." Niedernhofer L.J., Garinis G.A., Raams A., Lalai A.S., Robinson A.R., Appeldoorn E., Odijk H., Oostendorp R., Ahmad A., van Leeuwen W., Theil A.F., Vermeulen W., van der Horst G.T.J., Meinecke P., Kleijer W.J., Vijg J., Jaspers N.G.J., Hoeijmakers J.H.J. Nature 444:1038-1043(2006) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT XFEPS PRO-153. |
| + | Additional computationally mapped references. |
Web resources
Cross-references
Sequence databases | |||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EMBL GenBank DDBJ | L77890 Genomic DNA. Translation: AAB50174.1. AK289726 mRNA. Translation: BAF82415.1. AF491814 Genomic DNA. Translation: AAL91593.1. U64315 mRNA. Translation: AAB07689.1. Different initiation. | ||||||||||||||||||||||||||||||
| IPI | IPI00219179. | ||||||||||||||||||||||||||||||
| RefSeq | NP_005227.1. NM_005236.2. | ||||||||||||||||||||||||||||||
| UniGene | Hs.567265. | ||||||||||||||||||||||||||||||
3D structure databases | |||||||||||||||||||||||||||||||
| PDBe RCSB PDB PDBj |
| ||||||||||||||||||||||||||||||
| ProteinModelPortal | Q92889. | ||||||||||||||||||||||||||||||
| ModBase | Search... | ||||||||||||||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||||||||||||||
| DIP | DIP-42006N. | ||||||||||||||||||||||||||||||
| IntAct | Q92889. 4 interactions. | ||||||||||||||||||||||||||||||
| STRING | 9606.ENSP00000310520. | ||||||||||||||||||||||||||||||
PTM databases | |||||||||||||||||||||||||||||||
| PhosphoSite | Q92889. | ||||||||||||||||||||||||||||||
Polymorphism databases | |||||||||||||||||||||||||||||||
| DMDM | 229463004. | ||||||||||||||||||||||||||||||
Proteomic databases | |||||||||||||||||||||||||||||||
| PaxDb | Q92889. | ||||||||||||||||||||||||||||||
| PRIDE | Q92889. | ||||||||||||||||||||||||||||||
Protocols and materials databases | |||||||||||||||||||||||||||||||
| DNASU | 2072. | ||||||||||||||||||||||||||||||
| StructuralBiologyKnowledgebase | Search... | ||||||||||||||||||||||||||||||
Genome annotation databases | |||||||||||||||||||||||||||||||
| Ensembl | ENST00000311895; ENSP00000310520; ENSG00000175595. | ||||||||||||||||||||||||||||||
| GeneID | 2072. | ||||||||||||||||||||||||||||||
| KEGG | hsa:2072. | ||||||||||||||||||||||||||||||
| UCSC | uc002dce.2. human. | ||||||||||||||||||||||||||||||
Organism-specific databases | |||||||||||||||||||||||||||||||
| CTD | 2072. | ||||||||||||||||||||||||||||||
| GeneCards | GC16P014014. | ||||||||||||||||||||||||||||||
| H-InvDB | HIX0038603. HIX0173284. | ||||||||||||||||||||||||||||||
| HGNC | HGNC:3436. ERCC4. | ||||||||||||||||||||||||||||||
| HPA | CAB000156. | ||||||||||||||||||||||||||||||
| MIM | 133520. gene. 278760. phenotype. 610965. phenotype. | ||||||||||||||||||||||||||||||
| neXtProt | NX_Q92889. | ||||||||||||||||||||||||||||||
| Orphanet | 276264. Xeroderma pigmentosum complementation group F. | ||||||||||||||||||||||||||||||
| PharmGKB | PA27850. | ||||||||||||||||||||||||||||||
| GenAtlas | Search... | ||||||||||||||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||||||||||||||
| eggNOG | COG1948. | ||||||||||||||||||||||||||||||
| HOGENOM | HOG000202204. | ||||||||||||||||||||||||||||||
| HOVERGEN | HBG051500. | ||||||||||||||||||||||||||||||
| InParanoid | Q92889. | ||||||||||||||||||||||||||||||
| KO | K10848. | ||||||||||||||||||||||||||||||
| OMA | QQSIVVD. | ||||||||||||||||||||||||||||||
Enzyme and pathway databases | |||||||||||||||||||||||||||||||
| Reactome | REACT_216. DNA Repair. | ||||||||||||||||||||||||||||||
Gene expression databases | |||||||||||||||||||||||||||||||
| ArrayExpress | Q92889. | ||||||||||||||||||||||||||||||
| Bgee | Q92889. | ||||||||||||||||||||||||||||||
| CleanEx | HS_ERCC4. | ||||||||||||||||||||||||||||||
| Genevestigator | Q92889. | ||||||||||||||||||||||||||||||
| GermOnline | ENSG00000175595. Homo sapiens. | ||||||||||||||||||||||||||||||
Family and domain databases | |||||||||||||||||||||||||||||||
| Gene3D | 3.40.50.10130. 1 hit. | ||||||||||||||||||||||||||||||
| InterPro | IPR020819. DNA_repair_nuc_XPF/helicase. IPR006166. ERCC4_domain. IPR006167. Rad1. IPR011335. Restrct_endonuc-II-like. IPR010994. RuvA_2-like. [Graphical view] | ||||||||||||||||||||||||||||||
| Pfam | PF02732. ERCC4. 1 hit. [Graphical view] | ||||||||||||||||||||||||||||||
| SMART | SM00891. ERCC4. 1 hit. [Graphical view] | ||||||||||||||||||||||||||||||
| SUPFAM | SSF52980. Restrict_endonuc_II-like_core. 1 hit. SSF47781. RuvA_2_like. 1 hit. | ||||||||||||||||||||||||||||||
| TIGRFAMs | TIGR00596. rad1. 1 hit. | ||||||||||||||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||||||||||||||
Other | |||||||||||||||||||||||||||||||
| EvolutionaryTrace | Q92889. | ||||||||||||||||||||||||||||||
| GenomeRNAi | 2072. | ||||||||||||||||||||||||||||||
| NextBio | 8429. | ||||||||||||||||||||||||||||||
| SOURCE | Search... | ||||||||||||||||||||||||||||||
Entry information
| Entry name | XPF_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q92889 Secondary accession number(s): A8K111, O00140, Q8TD83 | ||||||||
| Entry history |
| ||||||||
| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Chordata Protein Annotation Program | ||||||||
| Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. | ||||||||
Relevant documents
| Human chromosome 16 Human chromosome 16: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with
