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21  structures 569  species 3  interactions 2052  sequences 37  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

XPG_I
PDB 1a77 EBI.jpg
flap endonuclease-1 from methanococcus jannaschii
Identifiers
Symbol XPG_I
Pfam PF00867
Pfam clan CL0464
InterPro IPR006086
PROSITE PDOC00658
SCOP 1a77
SUPERFAMILY 1a77

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

  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. doi:10.1016/j.biochi.2003.10.014. PMID 14726017. 

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.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

XPG I-region Provide feedback

No Pfam abstract.

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 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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(207)
Full
(2052)
Representative proteomes NCBI
(1927)
Meta
(247)
RP15
(441)
RP35
(726)
RP55
(1045)
RP75
(1236)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(207)
Full
(2052)
Representative proteomes NCBI
(1927)
Meta
(247)
RP15
(441)
RP35
(726)
RP55
(1045)
RP75
(1236)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(207)
Full
(2052)
Representative proteomes NCBI
(1927)
Meta
(247)
RP15
(441)
RP35
(726)
RP55
(1045)
RP75
(1236)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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.

Note: You can also download the data file for the tree.

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 View help on the curation process

Seed source: Pfam-B_776 (release 3.0)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 207
Number in full: 2052
Average length of the domain: 87.50 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 14.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.5 22.5
Trusted cut-off 22.5 22.6
Noise cut-off 22.4 22.4
Model length: 94
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

XPG_I PCNA_C XPG_N

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 21 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 seqence.

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