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74  structures 1822  species 0  interactions 8310  sequences 199  architectures

Family: XPG_I (PF00867)

Summary: XPG I-region

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This is the Wikipedia entry entitled "XPG I protein domain". More...

XPG I protein domain Edit Wikipedia article

PDB 1a77 EBI.jpg
flap endonuclease-1 from methanococcus jannaschii
Symbol XPG_I
Pfam PF00867
Pfam clan CL0464
InterPro IPR006086
SCOP 1a77
CDD cd09868

In molecular biology, the XPG-I is a protein domain found on Xeroderma Pigmentosum Complementation Group G (XPG) protein.[1] The XPG protein is an endonuclease which repairs DNA damage caused by ultraviolet light (UV light). The XPG protein repairs DNA by a process called, Nucleotide excision repair. Mutations in the protein commonly cause Xeroderma Pigmentosum which often lead to skin cancer.


The function of the internal XPG (XPG-I) domain contains many of cysteine and glutamate amino acid residues that are frequently found in various enzyme active sites, DNA nucleases. The I domain, together with the N-terminal forms the catalytic domain that contains the active site.[2]


XPG cleaves the 5'-overhanging flap structure that is generated when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It has both 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.


  1. ^ O'Donovan A, Scherly D, Clarkson SG, Wood RD (1994). "Isolation of active recombinant XPG protein, a human DNA repair endonuclease.". J Biol Chem. 269 (23): 15965–8. PMID 8206890. 
  2. ^ Clarkson SG (2003). "The XPG story.". Biochimie. 85 (11): 1113–21. PMID 14726017. doi:10.1016/j.biochi.2003.10.014. 

This article incorporates text from the public domain Pfam and InterPro IPR006086

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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XPG I-region Provide feedback

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Literature references

  1. Shen B, Qiu J, Hosfield D, Tainer JA; , Trends Biochem Sci 1998;23:171-173.: Flap endonuclease homologs in archaebacteria exist as independent proteins. PUBMED:9612080 EPMC:9612080

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006086

This entry represents a domain found on Xeroderma Pigmentosum Complementation Group G (XPG) protein [ PUBMED:8206890 ]. XPG is a DNA endonuclease involved in DNA excision repair [ PUBMED:8078765 ]. The internal XPG (XPG-I) domain contains many cysteine and glutamate amino acid residues that are frequently found in various enzyme active sites of DNA nucleases. The I domain, together with the N-terminal, forms the catalytic domain that contains the active site [ PUBMED:14726017 ].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan 5_3_exonuc_C (CL0464), which has the following description:

This superfamily includes C-terminal domains from a number of DNA-processing enzymes including T4 RNase H, 5' to 3' exonuclease domain of DNA polymerase Taq, T5 5'-exonuclease, Flap endonuclease-1 (Fen-1 nuclease), and other eukaryotic endonucleases.

The clan contains the following 4 members:

5_3_exonuc RNaseH_C XPG_I XPG_I_2


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_776 (release 3.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 107
Number in full: 8310
Average length of the domain: 85.10 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 11.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.9 24.9
Trusted cut-off 24.9 24.9
Noise cut-off 24.8 24.8
Model length: 91
Family (HMM) version: 20
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Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the XPG_I domain has been found. There are 74 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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