Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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XPGI Xeroderma pigmentosum G I-region

SMART accession number:	SM00484
Description:	domain in nucleases
Interpro abstract (IPR006086):	This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.
GO process:	DNA repair (GO:0006281)
GO function:	nuclease activity (GO:0004518)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 793 XPGI domains in 792 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a XPGI domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with XPGI domain is also avaliable.

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Cooper PK, Nouspikel T, Clarkson SG, Leadon SA
  • Defective transcription-coupled repair of oxidative base damage in Cockayne syndrome patients from XP group G.
  • Science. 1997; 275: 990-3
  • Display abstract

  • In normal human cells, damage due to ultraviolet light is preferentially removed from active genes by nucleotide excision repair (NER) in a transcription-coupled repair (TCR) process that requires the gene products defective in Cockayne syndrome (CS). Oxidative damage, including thymine glycols, is shown to be removed by TCR in cells from normal individuals and from xeroderma pigmentosum (XP)-A, XP-F, and XP-G patients who have NER defects but not from XP-G patients who have severe CS. Thus, TCR of oxidative damage requires an XPG function distinct from its NER endonuclease activity. These results raise the possibility that defective TCR of oxidative damage contributes to the developmental defects associated with CS.

  • Tanaka K, Wood RD
  • Xeroderma pigmentosum and nucleotide excision repair of DNA.
  • Trends Biochem Sci. 1994; 19: 83-6
  • Display abstract

  • Nucleotide excision repair is a versatile strategy for removing DNA damage from the genome. Tremendous progress in understanding this process has been made in the last few years, and the field continues to develop rapidly. Exciting connections have emerged between nucleotide excision repair, transcription, and DNA replication, but many mysteries remain concerning the biochemical details of the mechanism, the connection with several human inherited syndromes, and the role of DNA repair in preventing cancer.

• Disease (disease genes where sequence variants are found in this domain)

• SwissProt sequences and OMIM curated human diseases associated with missense mutations within the XPGI domain.

  Protein	Disease
  DNA repair protein complementing XP-G cells (P28715) (SMART)	OMIM:133530: Xeroderma pigmentosum, group G OMIM:278780:

• Metabolism (metabolic pathways involving proteins which contain this domain)

• % proteins involved KEGG pathway ID Description 100.00 map03030 DNA replication This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with XPGI domain which could be assigned to a KEGG orthologous group, and not all proteins containing XPGI domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of XPGI domains in PDB

  PDB code	Main view	Title
  1a76		Flap endonuclease-1 from methanococcus jannaschii
  1a77		Flap endonuclease-1 from methanococcus jannaschii
  1b43		Fen-1 from p. furiosus
  1mc8		Crystal structure of flap endonuclease-1 r42e mutant from pyrococcus horikoshii
  1rxv		Crystal structure of a. fulgidus fen-1 bound to dna
  1rxw		Crystal structure of a. fulgidus fen-1 bound to dna
  1ul1		Crystal structure of the human fen1-pcna complex
  2izo		Structure of an archaeal pcna1-pcna2-fen1 complex

• Links (links to other resources describing this domain)

• PFAM	XPG_I
  INTERPRO	IPR006086
  PROSITE	XPG_1

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