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
XPG_I | |||||||||
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![]() flap endonuclease-1 from methanococcus jannaschii
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Identifiers | |||||||||
Symbol | XPG_I | ||||||||
Pfam | PF00867 | ||||||||
Pfam clan | CL0464 | ||||||||
InterPro | IPR006086 | ||||||||
PROSITE | PDOC00658 | ||||||||
SCOP | 1a77 | ||||||||
SUPERFAMILY | 1a77 | ||||||||
CDD | cd09868 | ||||||||
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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.
Function
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]
Mechanism
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.
References
- ^ 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.
- ^ 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
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XPG I-region Provide feedback
No Pfam abstract.
Literature references
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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
SCOOP: | XPG_I_2 |
Similarity to PfamA using HHSearch: | XPG_I_2 |
External database links
HOMSTRAD: | XPG_NI |
PROSITE: | PDOC00658 |
SCOP: | 1a77 |
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
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | nuclease activity (GO:0004518) |
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_2Alignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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Seed (114) |
Full (6071) |
Representative proteomes | UniProt (9466) |
NCBI (10912) |
Meta (241) |
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RP15 (1783) |
RP35 (3433) |
RP55 (4754) |
RP75 (5785) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (114) |
Full (6071) |
Representative proteomes | UniProt (9466) |
NCBI (10912) |
Meta (241) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1783) |
RP35 (3433) |
RP55 (4754) |
RP75 (5785) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Trees
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
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_776 (release 3.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 114 |
Number in full: | 6071 |
Average length of the domain: | 88.20 aa |
Average identity of full alignment: | 33 % |
Average coverage of the sequence by the domain: | 12.05 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 94 | ||||||||||||
Family (HMM) version: | 18 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Structures
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 56 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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