Summary: 8-oxoguanine DNA glycosylase, N-terminal domain
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Oxoguanine glycosylase Edit Wikipedia article
|, HMMH, HMUTM, OGH1, 8-oxoguanine DNA glycosylase|
|RNA expression pattern|
|8-oxoguanine DNA glycosylase, N-terminal domain|
structure of catalytically inactive q315a human 8-oxoguanine glycosylase complexed to 8-oxoguanine dna
8-Oxoguanine glycosylase also known as OGG1 is a DNA glycosylase enzyme that, in humans, is encoded by the OGG1 gene. It is involved in base excision repair. It is found in bacterial, archaeal and eukaryotic species.
OGG1 is the primary enzyme responsible for the excision of 8-oxoguanine (8-oxoG), a mutagenic base byproduct that occurs as a result of exposure to reactive oxygen species (ROS). OGG1 is a bifunctional glycosylase, as it is able to both cleave the glycosidic bond of the mutagenic lesion and cause a strand break in the DNA backbone. Alternative splicing of the C-terminal region of this gene classifies splice variants into two major groups, type 1 and type 2, depending on the last exon of the sequence. Type 1 alternative splice variants end with exon 7 and type 2 end with exon 8. One set of spliced forms are designated 1a, 1b, 2a to 2e. All variants have the N-terminal region in common. Many alternative splice variants for this gene have been described, but the full-length nature for every variant has not been determined. In eukaryotes, the N-terminus of this gene contains a mitochondrial targeting signal, essential for mitochondrial localization. However, OGG1-1a also has a nuclear location signal at its C-terminal end that suppresses mitochondrial targeting and causes OGG1-1a to localize to the nucleus. The main form of OGG1 that localizes to the mitochondria is OGG1-2a. A conserved N-terminal domain contributes residues to the 8-oxoguanine binding pocket. This domain is organised into a single copy of a TBP-like fold.
Despite the presumed importance of this enzyme, mice lacking Ogg1 have been generated and found to have a normal lifespan, and Ogg1 knockout mice have a higher probability to develop cancer, whereas Mth1 gene disruption concomitantly suppresses lung cancer development in Ogg1-/- mice. Interestingly, mice lacking Ogg1 have been shown to be prone to increased body weight and obesity, as well as high-fat diet induced insulin resistance. There is some controversy as to whether deletion of Ogg1 actually leads to increased 8-oxo-dG levels: the HPLC-EC assay suggests up to 6 fold higher levels of 8-oxo-dG in nuclear DNA and 20-fold higher in mitochondrial DNA whereas the fappy-glycosylase assay indicates no change.
OGG1 deficiency and increased 8-oxo-dG in mice
Mice without a functional OGG1 gene have about a 5-fold increased level of 8-oxo-dG in their livers compared to mice with wild-type OGG1. Mice defective in OGG1 also have an increased risk for cancer. Kunisada et al. irradiated mice without a functional OGG1 gene (OGG1 knock-out mice) and wild-type mice three times a week for forty weeks with UVB light at a relatively low dose (not enough to cause skin redness). Both types of mice had high levels of 8-oxo-dG in their epidermal cells three hours after irradiation. However, 24 hours later, the majority of 8-oxo-dG was absent from the epidermal cells of the wild-type mice but 8-oxo-dG remained elevated in the epidermal cells of the OGG1 knock-out mice. The irradiated OGG1 knock-out mice had more than twice the level of skin tumors compared to irradiated wild-type mice, and the rate of malignancy within the tumors was higher in the OGG1 knock-out mice (73%) than in the wild-type mice (50%).
As reviewed by Valavanidis et al., increased levels of 8-oxo-dG in a tissue can serve as a biomarker of oxidative stress. They also noted that increased levels of 8-oxo-dG are frequently found during carcinogenesis.
In the figure showing examples of mouse colonic epithelium, the colonic epithelium from a mouse on a normal diet was found to have a low level of 8-oxo-dG in its colonic crypts (panel A). However, a mouse likely undergoing colonic tumorigenesis (due to deoxycholate added to its diet) was found to have a high level of 8-oxo-dG in its colonic epithelium (panel B). Deoxycholate increases intracellular production of reactive oxygen resulting in increased oxidative stress, and this can lead to tumorigenesis and carcinogenesis.
In a breast cancer study, the methylation level of the OGG1 promoter was found to be anti-correlated with expression level of OGG1 messenger RNA. This means that hypermethylation was associated with low expression of OGG1 and hypomethylation was correlated with over-expression of OGG1. Thus, OGG1 expression is under epigenetic control. Breast cancers with methylation levels of the OGG1 promoter that were more than two standard deviations either above or below the normal were each associated with reduced patient survival.
OGG1 is the primary enzyme responsible for the excision of 8-oxo-2'-deoxyguanosine (8-oxo-dG). Even when OGG1 expression is normal, the presence of 8-oxo-dG is mutagenic since OGG1 is not 100% effective. Yasui et al. examined the fate of 8-oxo-dG when this oxidized derivative of deoxyguanosine was inserted into a specific gene in 800 cells in culture. After replication of the cells, 8-oxo-dG was restored to G in 86% of the clones, probably reflecting accurate OGG1 base excision repair or translesion synthesis without mutation. G:C to T:A transversions occurred in 5.9% of the clones, single base deletions in 2.1% and G:C to C:G transversions in 1.2%. Together, these mutations were the most common, totalling 9.2% of the 14% of mutations generated at the site of the 8-oxo-dG insertion. Among the other mutations in the 800 clones analyzed, there were also 3 larger deletions, of sizes 6, 33 and 135 base pairs. Thus 8-oxo-dG can directly cause mutations, some of which may contribute to carcinogenesis.
If OGG1 expression is reduced in cells, increased mutagenesis, and therefore increased carcinogenesis would be expected. The table, below, lists cancers with reduced expression of OGG1.
|Cancer||Expression||Form of OGG1||8-oxo-dG||Evaluation method||Ref.|
|Head and neck cancer||Under-expression||OGG1-2a||-||messenger RNA|||
|Adenocarcinoma of gastric cardia||Under-expression||cytoplasmic||increased||immunohistochemistry|||
|Astrocytoma||Under-expression||total cell OGG1||-||messenger RNA|||
|Esophageal cancer||48% Under-expression||nuclear||increased||immunohistochemistry|||
OGG1 or OGG activity in blood, and cancer
OGG1 methylation levels in blood cells were measured in a prospective study of 582 US Veterans, median age 72, and followed for 13 years. High OGG1 methylation at a particular promoter region was associated with increased risk for any cancer, and in particular for risk of prostate cancer.
Enzymatic activity excising 8-oxoguanine from DNA (OGG activity) was reduced in peripheral blood mononuclear cells (PBMCs), and in paired lung tissue, from patients with non–small cell lung cancer. OGG activity was also reduced in PBMCs of patients with head and neck squamous cell carcinoma (HNSCC).
- "Human PubMed Reference:".
- "Mouse PubMed Reference:".
- Nishioka K, Ohtsubo T, Oda H, Fujiwara T, Kang D, Sugimachi K, Nakabeppu Y (1999). "Expression and differential intracellular localization of two major forms of human 8-oxoguanine DNA glycosylase encoded by alternatively spliced OGG1 mRNAs". Mol. Biol. Cell. 10 (5): 1637–52. doi:10.1091/mbc.10.5.1637. PMC . PMID 10233168.
- "Entrez Gene: OGG1 8-oxoguanine DNA glycosylase".
- Bjørås M, Seeberg E, Luna L, Pearl LH, Barrett TE (March 2002). "Reciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase". J. Mol. Biol. 317 (2): 171–7. doi:10.1006/jmbi.2002.5400. PMID 11902834.
- Klungland A, Rosewell I, Hollenbach S, Larsen E, Daly G, Epe B, Seeberg E, Lindahl T, Barnes DE (November 1999). "Accumulation of premutagenic DNA lesions in mice defective in removal of oxidative base damage". Proc. Natl. Acad. Sci. U.S.A. 96 (23): 13300–5. doi:10.1073/pnas.96.23.13300. PMC . PMID 10557315.
- Sakumi K, Tominaga Y, Furuichi M, Xu P, Tsuzuki T, Sekiguchi M, Nakabeppu Y (2003). "Ogg1 knockout-associated lung tumorigenesis and its suppression by Mth1 gene disruption". Cancer Res. 63 (5): 902–5. PMID 12615700.
- Sampath H, Vartanian V, Rollins MR, Sakumi K, Nakabeppu Y, Lloyd RS (December 2012). "8-Oxoguanine DNA glycosylase (OGG1) deficiency increases susceptibility to obesity and metabolic dysfunction". PLoS ONE. 7 (12): e51697. doi:10.1371/journal.pone.0051697. PMC . PMID 23284747.
- Prasad AR, Prasad S, Nguyen H, Facista A, Lewis C, Zaitlin B, Bernstein H, Bernstein C (2014). "Novel diet-related mouse model of colon cancer parallels human colon cancer". World J Gastrointest Oncol. 6 (7): 225–43. doi:10.4251/wjgo.v6.i7.225. PMC . PMID 25024814.
- Kunisada M, Sakumi K, Tominaga Y, Budiyanto A, Ueda M, Ichihashi M, Nakabeppu Y, Nishigori C (2005). "8-Oxoguanine formation induced by chronic UVB exposure makes Ogg1 knockout mice susceptible to skin carcinogenesis". Cancer Res. 65 (14): 6006–10. doi:10.1158/0008-5472.CAN-05-0724. PMID 16024598.
- Valavanidis A, Vlachogianni T, Fiotakis K, Loridas S (2013). "Pulmonary oxidative stress, inflammation and cancer: respirable particulate matter, fibrous dusts and ozone as major causes of lung carcinogenesis through reactive oxygen species mechanisms". Int J Environ Res Public Health. 10 (9): 3886–907. doi:10.3390/ijerph10093886. PMC . PMID 23985773.
- Tsuei J, Chau T, Mills D, Wan YJ. Bile acid dysregulation, gut dysbiosis, and gastrointestinal cancer. Exp Biol Med (Maywood). 2014 Nov;239(11):1489-504. doi: 10.1177/1535370214538743. PMID 24951470
- Ajouz H, Mukherji D, Shamseddine A. Secondary bile acids: an underrecognized cause of colon cancer. World J Surg Oncol. 2014 May 24;12:164. doi: 10.1186/1477-7819-12-164. Review. PMID 24884764
- Fleischer T, Edvardsen H, Solvang HK, Daviaud C, Naume B, Børresen-Dale AL, Kristensen VN, Tost J (2014). "Integrated analysis of high-resolution DNA methylation profiles, gene expression, germline genotypes and clinical end points in breast cancer patients". Int. J. Cancer. 134 (11): 2615–25. doi:10.1002/ijc.28606. PMID 24395279.
- Yasui M, Kanemaru Y, Kamoshita N, Suzuki T, Arakawa T, Honma M (2014). "Tracing the fates of site-specifically introduced DNA adducts in the human genome". DNA Repair (Amst.). 15: 11–20. doi:10.1016/j.dnarep.2014.01.003. PMID 24559511.
- Mahjabeen I, Kayani MA (2016). "Loss of Mitochondrial Tumor Suppressor Genes Expression Is Associated with Unfavorable Clinical Outcome in Head and Neck Squamous Cell Carcinoma: Data from Retrospective Study". PLoS ONE. 11 (1): e0146948. doi:10.1371/journal.pone.0146948. PMC . PMID 26785117.
- Kohno Y, Yamamoto H, Hirahashi M, Kumagae Y, Nakamura M, Oki E, Oda Y (2016). "Reduced MUTYH, MTH1, and OGG1 expression and TP53 mutation in diffuse-type adenocarcinoma of gastric cardia". Hum. Pathol. 52: 145–52. doi:10.1016/j.humpath.2016.01.006. PMID 26980051.
- Jiang Z, Hu J, Li X, Jiang Y, Zhou W, Lu D (2006). "Expression analyses of 27 DNA repair genes in astrocytoma by TaqMan low-density array". Neurosci. Lett. 409 (2): 112–7. doi:10.1016/j.neulet.2006.09.038. PMID 17034947.
- Kubo N, Morita M, Nakashima Y, Kitao H, Egashira A, Saeki H, Oki E, Kakeji Y, Oda Y, Maehara Y (2014). "Oxidative DNA damage in human esophageal cancer: clinicopathological analysis of 8-hydroxydeoxyguanosine and its repair enzyme". Dis. Esophagus. 27 (3): 285–93. doi:10.1111/dote.12107. PMID 23902537.
- Gao T, Joyce BT, Liu L, Zheng Y, Dai Q, Zhang Z, Zhang W, Shrubsole MJ, Tao MH, Schwartz J, Baccarelli A, Hou L (2016). "DNA methylation of oxidative stress genes and cancer risk in the Normative Aging Study". Am J Cancer Res. 6 (2): 553–61. PMC . PMID 27186424.
- Paz-Elizur T, Krupsky M, Blumenstein S, Elinger D, Schechtman E, Livneh Z (2003). "DNA repair activity for oxidative damage and risk of lung cancer". J. Natl. Cancer Inst. 95 (17): 1312–9. doi:10.1093/jnci/djg033. PMID 12953085.
- Paz-Elizur T, Ben-Yosef R, Elinger D, Vexler A, Krupsky M, Berrebi A, Shani A, Schechtman E, Freedman L, Livneh Z (2006). "Reduced repair of the oxidative 8-oxoguanine DNA damage and risk of head and neck cancer". Cancer Res. 66 (24): 11683–9. doi:10.1158/0008-5472.CAN-06-2294. PMID 17178863.
- Marsin S, Vidal AE, Sossou M, Ménissier-de Murcia J, Le Page F, Boiteux S, de Murcia G, Radicella JP (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.
- Dantzer F, Luna L, Bjørås M, Seeberg E (June 2002). "Human OGG1 undergoes serine phosphorylation and associates with the nuclear matrix and mitotic chromatin in vivo". Nucleic Acids Res. 30 (11): 2349–57. doi:10.1093/nar/30.11.2349. PMC . PMID 12034821.
- Osorio A, Milne RL, Kuchenbaecker K, Vaclová T, Pita G, Alonso R, Peterlongo P, Blanco I, de la Hoya M, Duran M, Díez O, Ramón Y, Cajal T, Konstantopoulou I, Martínez-Bouzas C, Andrés Conejero R, Soucy P, McGuffog L, Barrowdale D, Lee A, Arver B, Rantala J, Loman N, Ehrencrona H, Olopade OI, Beattie MS, Domchek SM, Nathanson K, Rebbeck TR, Arun BK, Karlan BY, Walsh C, Lester J, John EM, Whittemore AS, Daly MB, Southey M, Hopper J, Terry MB, Buys SS, Janavicius R, Dorfling CM, van Rensburg EJ, Steele L, Neuhausen SL, Ding YC, Hansen TV, Jønson L, Ejlertsen B, Gerdes AM, Infante M, Herráez B, Moreno LT, Weitzel JN, Herzog J, Weeman K, Manoukian S, Peissel B, Zaffaroni D, Scuvera G, Bonanni B, Mariette F, Volorio S, Viel A, Varesco L, Papi L, Ottini L, Tibiletti MG, Radice P, Yannoukakos D, Garber J, Ellis S, Frost D, Platte R, Fineberg E, Evans G, Lalloo F, Izatt L, Eeles R, Adlard J, Davidson R, Cole T, Eccles D, Cook J, Hodgson S, Brewer C, Tischkowitz M, Douglas F, Porteous M, Side L, Walker L, Morrison P, Donaldson A, Kennedy J, Foo C, Godwin AK, Schmutzler RK, Wappenschmidt B, Rhiem K, Engel C, Meindl A, Ditsch N, Arnold N, Plendl HJ, Niederacher D, Sutter C, Wang-Gohrke S, Steinemann D, Preisler-Adams S, Kast K, Varon-Mateeva R, Gehrig A, Stoppa-Lyonnet D, Sinilnikova OM, Mazoyer S, Damiola F, Poppe B, Claes K, Piedmonte M, Tucker K, Backes F, Rodríguez G, Brewster W, Wakeley K, Rutherford T, Caldés T, Nevanlinna H, Aittomäki K, Rookus MA, van Os TA, van der Kolk L, de Lange JL, Meijers-Heijboer HE, van der Hout AH, van Asperen CJ, Gómez Garcia EB, Hoogerbrugge N, Collée JM, van Deurzen CH, van der Luijt RB, Devilee P, Olah E, Lázaro C, Teulé A, Menéndez M, Jakubowska A, Cybulski C, Gronwald J, Lubinski J, Durda K, Jaworska-Bieniek K, Johannsson OT, Maugard C, Montagna M, Tognazzo S, Teixeira MR, Healey S, Investigators K, Olswold C, Guidugli L, Lindor N, Slager S, Szabo CI, Vijai J, Robson M, Kauff N, Zhang L, Rau-Murthy R, Fink-Retter A, Singer CF, Rappaport C, Geschwantler Kaulich D, Pfeiler G, Tea MK, Berger A, Phelan CM, Greene MH, Mai PL, Lejbkowicz F, Andrulis I, Mulligan AM, Glendon G, Toland AE, Bojesen A, Pedersen IS, Sunde L, Thomassen M, Kruse TA, Jensen UB, Friedman E, Laitman Y, Shimon SP, Simard J, Easton DF, Offit K, Couch FJ, Chenevix-Trench G, Antoniou AC, Benitez J (2014). "DNA glycosylases involved in base excision repair may be associated with cancer risk in BRCA1 and BRCA2 mutation carriers". PLoS Genet. 10 (4): e1004256. doi:10.1371/journal.pgen.1004256. PMC . PMID 24698998.
- Boiteux S, Radicella JP (2000). "The human OGG1 gene: structure, functions, and its implication in the process of carcinogenesis". Arch. Biochem. Biophys. 377 (1): 1–8. doi:10.1006/abbi.2000.1773. PMID 10775435.
- Park J, Chen L, Tockman MS, Elahi A, Lazarus P (2004). "The human 8-oxoguanine DNA N-glycosylase 1 (hOGG1) DNA repair enzyme and its association with lung cancer risk". Pharmacogenetics. 14 (2): 103–9. doi:10.1097/00008571-200402000-00004. PMID 15077011.
- Hung RJ, Hall J, Brennan P, Boffetta P (2005). "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.
- Mirbahai L, Kershaw RM, Green RM, Hayden RE, Meldrum RA, Hodges NJ (2010). "Use of a molecular beacon to track the activity of base excision repair protein OGG1 in live cells". DNA Repair (Amst.). 9 (2): 144–52. doi:10.1016/j.dnarep.2009.11.009. PMID 20042377.
- oxoguanine glycosylase 1, human at the US National Library of Medicine Medical Subject Headings (MeSH)
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8-oxoguanine DNA glycosylase, N-terminal domain Provide feedback
The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity ( EC:220.127.116.11) and DNA lyase activity ( EC:18.104.22.168) . The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket .
Bjoras M, Seeberg E, Luna L, Pearl LH, Barrett TE; , J Mol Biol 2002;317:171-177.: Reciprocal "flipping" underlies substrate recognition and catalytic activation by the human 8-oxo-guanine DNA glycosylase. PUBMED:11902834 EPMC:11902834
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This tab holds annotation information from the InterPro database.
InterPro entry IPR012904
The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (EC) and DNA lyase activity (EC) [PUBMED:10706276]. The region featured in this family is the N-terminal domain, which is organised into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket [PUBMED:11902834].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||damaged DNA binding (GO:0003684)|
|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)|
|Biological process||nucleotide-excision repair (GO:0006289)|
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TBP is a transcription factor whose DNA binding fold is composed of a curved antiparallel beta-sheet . This fold is also found in the N terminal region of DNA repair glycosylases. The N terminal domain of DNA glycosylase has only a single copy of the fold, whereas TBP contains a duplication of this fold [2-3].
The clan contains the following 5 members:AlkA_N DUF3378 OGG_N Rep_trans TBP
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|Seed source:||Pfam-B_29151 (release 14.0)|
|Number in seed:||59|
|Number in full:||1230|
|Average length of the domain:||116.90 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||27.46 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
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.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
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.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
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.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
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.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 OGG_N domain has been found. There are 36 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.
Loading structure mapping...