Summary: XRCC1 N terminal domain
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XRCC1 Edit Wikipedia article
|X-ray repair complementing defective repair in Chinese hamster cells 1|
PDB rendering based on 1cdz.
|RNA expression pattern|
DNA repair protein XRCC1 also known as X-ray repair cross-complementing protein 1 is a protein that in humans is encoded by the XRCC1 gene. XRCC1 is involved in DNA repair where it complexes with DNA ligase III.
XRCC1 is involved in the efficient repair of DNA single-strand breaks formed by exposure to ionizing radiation and alkylating agents. This protein interacts with DNA ligase III, polymerase beta and poly (ADP-ribose) polymerase to participate in the base excision repair pathway. It may play a role in DNA processing during meiogenesis and recombination in germ cells. A rare microsatellite polymorphism in this gene is associated with cancer in patients of varying radiosensitivity.
The NMR solution structure of the Xrcc1 N-terminal domain (Xrcc1 NTD) shows that the structural core is a beta-sandwich with beta-strands connected by loops, three helices and two short two-stranded beta-sheets at each connection side. The Xrcc1 NTD specifically binds single-strand break DNA (gapped and nicked) and a gapped DNA-beta-Pol complex.
XRCC1 has been shown to interact with:
- POLB, and
- Rice PA (September 1999). "Holding damaged DNA together". Nat. Struct. Biol. 6 (9): 805–6. doi:10.1038/12257. PMID 10467087.
- "Entrez Gene: XRCC1 X-ray repair complementing defective repair in Chinese hamster cells 1".
- Marintchev A, Mullen MA, Maciejewski MW, Pan B, Gryk MR, Mullen GP (September 1999). "Solution structure of the single-strand break repair protein XRCC1 N-terminal domain". Nat. Struct. Biol. 6 (9): 884–93. doi:10.1038/12347. PMID 10467102.
- Vidal AE, Boiteux S, Hickson I D, Radicella J P (November 2001). "XRCC1 coordinates the initial and late stages of DNA abasic site repair through protein-protein interactions". EMBO J. 20 (22): 6530–9. doi:10.1093/emboj/20.22.6530. PMC 125722. PMID 11707423.
- Date H, Igarashi Shuichi, Sano Yasuteru, Takahashi Toshiaki, Takahashi Tetsuya, Takano Hiroki, Tsuji Shoji, Nishizawa Masatoyo, Onodera Osamu (Dec 2004). "The FHA domain of aprataxin interacts with the C-terminal region of XRCC1". Biochem. Biophys. Res. Commun. 325 (4): 1279–85. doi:10.1016/j.bbrc.2004.10.162. PMID 15555565.
- Gueven N, Becherel Olivier J, Kijas Amanda W, Chen Philip, Howe Orla, Rudolph Jeanette H, Gatti Richard, Date Hidetoshi, Onodera Osamu, Taucher-Scholz Gisela, Lavin Martin F (May 2004). "Aprataxin, a novel protein that protects against genotoxic stress". Hum. Mol. Genet. 13 (10): 1081–93. doi:10.1093/hmg/ddh122. PMID 15044383.
- Marsin Sé, Vidal Antonio E, Sossou Marguerite, Ménissier-de Murcia Josiane, Le Page Florence, Boiteux Serge, de Murcia Gilbert, Radicella J Pablo (November 2003). "Role of XRCC1 in the coordination and stimulation of oxidative DNA damage repair initiated by the DNA glycosylase hOGG1". J. Biol. Chem. 278 (45): 44068–74. doi:10.1074/jbc.M306160200. PMID 12933815.
- Schreiber Vé, Amé Jean-Christophe, Dollé Pascal, Schultz Inès, Rinaldi Bruno, Fraulob Valérie, Ménissier-de Murcia Josiane, de Murcia Gilbert (June 2002). "Poly(ADP-ribose) polymerase-2 (PARP-2) is required for efficient base excision DNA repair in association with PARP-1 and XRCC1". J. Biol. Chem. 277 (25): 23028–36. doi:10.1074/jbc.M202390200. PMID 11948190.
- Fan J, Otterlei Marit, Wong Heng-Kuan, Tomkinson Alan E, Wilson David M (2004). "XRCC1 co-localizes and physically interacts with PCNA". Nucleic Acids Res. 32 (7): 2193–201. doi:10.1093/nar/gkh556. PMC 407833. PMID 15107487.
- Whitehouse CJ, Taylor R M, Thistlethwaite A, Zhang H, Karimi-Busheri F, Lasko D D, Weinfeld M, Caldecott K W (January 2001). "XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair". Cell 104 (1): 107–17. doi:10.1016/S0092-8674(01)00195-7. PMID 11163244.
- Ewing RM, Chu Peter, Elisma Fred, Li Hongyan, Taylor Paul, Climie Shane, McBroom-Cerajewski Linda, Robinson Mark D, O'Connor Liam, Li Michael, Taylor Rod, Dharsee Moyez, Ho Yuen, Heilbut Adrian, Moore Lynda, Zhang Shudong, Ornatsky Olga, Bukhman Yury V, Ethier Martin, Sheng Yinglun, Vasilescu Julian, Abu-Farha Mohamed, Lambert Jean-Philippe, Duewel Henry S, Stewart Ian I, Kuehl Bonnie, Hogue Kelly, Colwill Karen, Gladwish Katharine, Muskat Brenda, Kinach Robert, Adams Sally-Lin, Moran Michael F, Morin Gregg B, Topaloglou Thodoros, Figeys Daniel (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931.
- Wang L, Bhattacharyya Nandan, Chelsea Diane M, Escobar Pedro F, Banerjee Sipra (November 2004). "A novel nuclear protein, MGC5306 interacts with DNA polymerase beta and has a potential role in cellular phenotype". Cancer Res. 64 (21): 7673–7. doi:10.1158/0008-5472.CAN-04-2801. PMID 15520167.
- Kubota Y, Nash R A, Klungland A, Schär P, Barnes D E, Lindahl T (Dec 1996). "Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase beta and the XRCC1 protein". EMBO J. 15 (23): 6662–70. PMC 452490. PMID 8978692.
- Bhattacharyya N, Banerjee S (July 2001). "A novel role of XRCC1 in the functions of a DNA polymerase beta variant". Biochemistry 40 (30): 9005–13. doi:10.1021/bi0028789. PMID 11467963.
- Masson M, Niedergang C, Schreiber V, Muller S, Menissier-de Murcia J, de Murcia G (June 1998). "XRCC1 is specifically associated with poly(ADP-ribose) polymerase and negatively regulates its activity following DNA damage". Mol. Cell. Biol. 18 (6): 3563–71. PMC 108937. PMID 9584196.
- Hung RJ, Hall J, Brennan P, Boffetta P (2006). "Genetic polymorphisms in the base excision repair pathway and cancer risk: a HuGE review.". Am. J. Epidemiol. 162 (10): 925–42. doi:10.1093/aje/kwi318. PMID 16221808.
- Thompson LH, Brookman KW, Jones NJ, et al. (1991). "Molecular cloning of the human XRCC1 gene, which corrects defective DNA strand break repair and sister chromatid exchange.". Mol. Cell. Biol. 10 (12): 6160–71. PMC 362891. PMID 2247054.
- Thompson LH, Bachinski LL, Stallings RL, et al. (1990). "Complementation of repair gene mutations on the hemizygous chromosome 9 in CHO: a third repair gene on human chromosome 19.". Genomics 5 (4): 670–9. doi:10.1016/0888-7543(89)90107-9. PMID 2591959.
- Gyapay G, Morissette J, Vignal A, et al. (1994). "The 1993-94 Généthon human genetic linkage map.". Nat. Genet. 7 (2 Spec No): 246–339. doi:10.1038/ng0694supp-246. PMID 7545953.
- Wei Q, Xu X, Cheng L, et al. (1995). "Simultaneous amplification of four DNA repair genes and beta-actin in human lymphocytes by multiplex reverse transcriptase-PCR.". Cancer Res. 55 (21): 5025–9. PMID 7585546.
- Lamerdin JE, Montgomery MA, Stilwagen SA, et al. (1995). "Genomic sequence comparison of the human and mouse XRCC1 DNA repair gene regions.". Genomics 25 (2): 547–54. doi:10.1016/0888-7543(95)80056-R. PMID 7789989.
- Caldecott KW, McKeown CK, Tucker JD, et al. (1994). "An interaction between the mammalian DNA repair protein XRCC1 and DNA ligase III.". Mol. Cell. Biol. 14 (1): 68–76. PMC 358357. PMID 8264637.
- Trask B, Fertitta A, Christensen M, et al. (1993). "Fluorescence in situ hybridization mapping of human chromosome 19: cytogenetic band location of 540 cosmids and 70 genes or DNA markers.". Genomics 15 (1): 133–45. doi:10.1006/geno.1993.1021. PMID 8432525.
- Kubota Y, Nash RA, Klungland A, et al. (1997). "Reconstitution of DNA base excision-repair with purified human proteins: interaction between DNA polymerase beta and the XRCC1 protein.". EMBO J. 15 (23): 6662–70. PMC 452490. PMID 8978692.
- Nash RA, Caldecott KW, Barnes DE, Lindahl T (1997). "XRCC1 protein interacts with one of two distinct forms of DNA ligase III.". Biochemistry 36 (17): 5207–11. doi:10.1021/bi962281m. PMID 9136882.
- Shen MR, Jones IM, Mohrenweiser H (1998). "Nonconservative amino acid substitution variants exist at polymorphic frequency in DNA repair genes in healthy humans.". Cancer Res. 58 (4): 604–8. PMID 9485007.
- Price EA, Bourne SL, Radbourne R, et al. (1998). "Rare microsatellite polymorphisms in the DNA repair genes XRCC1, XRCC3 and XRCC5 associated with cancer in patients of varying radiosensitivity.". Somat. Cell Mol. Genet. 23 (4): 237–47. doi:10.1007/BF02674415. PMID 9542526.
- Masson M, Niedergang C, Schreiber V, et al. (1998). "XRCC1 is specifically associated with poly(ADP-ribose) polymerase and negatively regulates its activity following DNA damage.". Mol. Cell. Biol. 18 (6): 3563–71. PMC 108937. PMID 9584196.
- Taylor RM, Wickstead B, Cronin S, Caldecott KW (1998). "Role of a BRCT domain in the interaction of DNA ligase III-alpha with the DNA repair protein XRCC1.". Curr. Biol. 8 (15): 877–80. doi:10.1016/S0960-9822(07)00350-8. PMID 9705932.
- Zhou ZQ, Walter CA (1998). "Cloning and characterization of the promoter of baboon XRCC1, a gene involved in DNA strand-break repair.". Somat. Cell Mol. Genet. 24 (1): 23–39. doi:10.1007/BF02677493. PMID 9776979.
- Taylor RM, Moore DJ, Whitehouse J, et al. (2000). "A cell cycle-specific requirement for the XRCC1 BRCT II domain during mammalian DNA strand break repair.". Mol. Cell. Biol. 20 (2): 735–40. doi:10.1128/MCB.20.2.735-740.2000. PMC 85188. PMID 10611252.
- Marintchev A, Robertson A, Dimitriadis EK, et al. (2000). "Domain specific interaction in the XRCC1-DNA polymerase beta complex.". Nucleic Acids Res. 28 (10): 2049–59. doi:10.1093/nar/28.10.2049. PMC 105377. PMID 10773072.
- Duell EJ, Wiencke JK, Cheng TJ, et al. (2000). "Polymorphisms in the DNA repair genes XRCC1 and ERCC2 and biomarkers of DNA damage in human blood mononuclear cells.". Carcinogenesis 21 (5): 965–71. doi:10.1093/carcin/21.5.965. PMID 10783319.
- Whitehouse CJ, Taylor RM, Thistlethwaite A, et al. (2001). "XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair.". Cell 104 (1): 107–17. doi:10.1016/S0092-8674(01)00195-7. PMID 11163244.
- Dulic A, Bates PA, Zhang X, et al. (2001). "BRCT domain interactions in the heterodimeric DNA repair protein XRCC1-DNA ligase III.". Biochemistry 40 (20): 5906–13. doi:10.1021/bi002701e. PMID 11352725.
- X-ray repair cross complementing protein 1 at the US National Library of Medicine Medical Subject Headings (MeSH)
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XRCC1 N terminal domain Provide feedback
No Pfam abstract.
Marintchev A, Mullen MA, Maciejewski MW, Pan B, Gryk MR, Mullen GP; , Nat Struct Biol 1999;6:884-893.: Solution structure of the single-strand break repair protein XRCC1 N- terminal domain. PUBMED:10467102 EPMC:10467102
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002706
DNA-repair protein Xrcc1 functions in the repair of single-strand DNA breaks in mammalian cells and forms a repair complex with beta-Pol, ligase III and PARP [PUBMED:10467087]. The NMR solution structure of the Xrcc1 N-terminal domain (Xrcc1 NTD) shows that the structural core is a beta-sandwich with beta-strands connected by loops, three helices and two short two-stranded beta-sheets at each connection side. The Xrcc1 NTD specifically binds single-strand break DNA (gapped and nicked) and a gapped DNA-beta-Pol complex [PUBMED:10467102].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||nucleus (GO:0005634)|
|Molecular function||damaged DNA binding (GO:0003684)|
|Biological process||single strand break repair (GO:0000012)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site .
The clan contains the following 27 members:Allantoicase APC10 Bac_rhamnosid_N BetaGal_dom4_5 CBM_11 CBM_15 CBM_17_28 CBM_4_9 CBM_6 CIA30 Cleaved_Adhesin DUF642 Endotoxin_C Ephrin_lbd F5_F8_type_C FBA Glyco_hydro_2_N Laminin_N Lyase_N MAM Muskelin_N P_proprotein PA-IL PepX_C PITH Sad1_UNC XRCC1_N
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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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|Number in seed:||3|
|Number in full:||182|
|Average length of the domain:||131.20 aa|
|Average identity of full alignment:||46 %|
|Average coverage of the sequence by the domain:||23.24 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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 XRCC1_N domain has been found. There are 13 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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