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1  structure 169  species 1  interaction 1069  sequences 46  architectures

Family: BRCA2 (PF00634)

Summary: BRCA2 repeat

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BRCA2
PBB Protein BRCA2 image.jpg
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases BRCA2, BRCC2, BROVCA2, FACD, FAD, FAD1, FANCD, FANCD1, GLM3, PNCA2, XRCC11, breast cancer 2
External IDs MGI: 109337 HomoloGene: 41 GeneCards: 675
RNA expression pattern
PBB GE BRCA2 208368 s at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_000059

NM_001081001
NM_009765

RefSeq (protein)

NP_000050.2

NP_001074470.1
NP_033895.2

Location (UCSC) Chr 13: 32.32 – 32.4 Mb Chr 5: 150.52 – 150.57 Mb
PubMed search [1] [2]
Wikidata
View/Edit Human View/Edit Mouse
BRCA2 repeat
PDB 1n0w EBI.jpg
crystal structure of a rad51-brca2 brc repeat complex
Identifiers
Symbol BRCA2
Pfam PF00634
InterPro IPR002093
SCOP 1n0w
SUPERFAMILY 1n0w
BRCA-2 helical
PDB 1miu EBI.jpg
structure of a brca2-dss1 complex
Identifiers
Symbol BRCA-2_helical
Pfam PF09169
InterPro IPR015252
SCOP 1iyj
SUPERFAMILY 1iyj
BRCA2, oligonucleotide/oligosaccharide-binding, domain 1
PDB 1miu EBI.jpg
structure of a brca2-dss1 complex
Identifiers
Symbol BRCA-2_OB1
Pfam PF09103
InterPro IPR015187
SCOP 1iyj
SUPERFAMILY 1iyj
BRCA2, oligonucleotide/oligosaccharide-binding, domain 3
PDB 1miu EBI.jpg
structure of a brca2-dss1 complex
Identifiers
Symbol BRCA-2_OB3
Pfam PF09104
InterPro IPR015188
SCOP 1iyj
SUPERFAMILY 1iyj
Tower domain
PDB 1miu EBI.jpg
structure of a brca2-dss1 complex
Identifiers
Symbol Tower
Pfam PF09121
InterPro IPR015205
SCOP 1mje
SUPERFAMILY 1mje

BRCA2 and BRCA2 (/ˌbrækəˈt/[1]) are a human gene and its protein product, respectively. The official symbol (BRCA2, italic for the gene, nonitalic for the protein) and the official name (breast cancer 2) are maintained by the HGNC. One alternative symbol, FANCD1, recognizes its association with the FANC protein complex. Orthologs, styled Brca2 and Brca2, are common in other mammal species.[2] BRCA2 is a human tumor suppressor gene[3][4] (specifically, a caretaker gene), found in all humans; its protein, also called by the synonym breast cancer type 2 susceptibility protein, is responsible for repairing DNA.[5]

BRCA2 and BRCA1 are normally expressed in the cells of breast and other tissue, where they help repair damaged DNA or destroy cells if DNA cannot be repaired. They are involved in the repair of chromosomal damage with an important role in the error-free repair of DNA double strand breaks.[6][7] If BRCA1 or BRCA2 itself is damaged by a BRCA mutation, damaged DNA is not repaired properly, and this increases the risk for breast cancer.[8][9] Thus, although the terms "breast cancer susceptibility gene" and "breast cancer susceptibility protein" (used frequently both in and outside the medical literature) sound as if they describe a proto-oncogene or oncogene, BRCA1 and BRCA2 are "normal"; it is their mutation that is abnormal.

The BRCA2 gene is located on the long (q) arm of chromosome 13 at position 12.3 (13q12.3).[10] The human reference BRCA 2 gene contains 28 exons, and the cDNA has 10,254 base pairs[11] coding for a protein of 3418 amino acids.[12][13]

The gene was first cloned by scientists at Myriad Genetics, Endo Recherche, Inc., HSC Research & Development Limited Partnership, and the University of Pennsylvania.[14]

Methods to diagnose the likelihood of a patient with mutations in BRCA1 and BRCA2 getting cancer were covered by patents owned or controlled by Myriad Genetics.[15][16] Myriad's business model of exclusively offering the diagnostic test led from Myriad being a startup in 1994 to being a publicly traded company with 1200 employees and about $500M in annual revenue in 2012;[17] it also led to controversy over high prices and the inability to get second opinions from other diagnostic labs, which in turn led to the landmark Association for Molecular Pathology v. Myriad Genetics lawsuit.[18]

Function

Recombinational repair of DNA double-strand damage - some key steps. ATM (ATM) is a protein kinase that is recruited and activated by DNA double-strand breaks. DNA double-strand damages also activate the Fanconi anemia core complex (FANCA/B/C/E/F/G/L/M).[19] The FA core complex monoubiquitinates the downstream targets FANCD2 and FANCI.[20] ATM activates (phosphorylates) CHEK2 and FANCD2[21] CHEK2 phosphorylates BRCA1.[22] Ubiquinated FANCD2 complexes with BRCA1 and RAD51.[23] The PALB2 protein acts as a hub,[24] bringing together BRCA1, BRCA2 and RAD51 at the site of a DNA double-strand break, and also binds to RAD51C, a member of the RAD51 paralog complex RAD51B-RAD51C-RAD51D-XRCC2 (BCDX2). The BCDX2 complex is responsible for RAD51 recruitment or stabilization at damage sites.[25] RAD51 plays a major role in homologous recombinational repair of DNA during double strand break repair. In this process, an ATP dependent DNA strand exchange takes place in which a single strand invades base-paired strands of homologous DNA molecules. RAD51 is involved in the search for homology and strand pairing stages of the process.

Although the structures of the BRCA1 and BRCA2 genes are very different, at least some functions are interrelated. The proteins made by both genes are essential for repairing damaged DNA (see Figure of recombinational repair steps). BRCA2 binds the single strand DNA and directly interacts with the recombinase RAD51 to stimulate strand invasion a vital step of homologous recombination. The localization of RAD51 to the DNA double-strand break requires the formation of BRCA1-PALB2-BRCA2 complex. PALB2 (Partner and localizer of BRCA2)[26] can function synergistically with a BRCA2 chimera (termed piccolo, or piBRCA2) to further promote strand invasion.[27] These breaks can be caused by natural and medical radiation or other environmental exposures, but also occur when chromosomes exchange genetic material during a special type of cell division that creates sperm and eggs (meiosis). Double strand breaks are also generated during repair of DNA cross links. By repairing DNA, these proteins play a role in maintaining the stability of the human genome and prevent dangerous gene rearrangements that can lead to hematologic and other cancers.

Like BRCA1, BRCA2 probably regulates the activity of other genes and plays a critical role in embryo development.

Clinical significance

Further information: BRCA mutation

Certain variations of the BRCA2 gene increase risks for breast cancer as part of a hereditary breast-ovarian cancer syndrome. Researchers have identified hundreds of mutations in the BRCA2 gene, many of which cause an increased risk of cancer. BRCA2 mutations are usually insertions or deletions of a small number of DNA base pairs in the gene. As a result of these mutations, the protein product of the BRCA2 gene is abnormal and does not function properly. Researchers believe that the defective BRCA2 protein is unable to fix DNA damages that occur throughout the genome. As a result, there is an increase in mutations due to error-prone translesion synthesis past un-repaired DNA damages, and some of these mutations can cause cells to divide in an uncontrolled way and form a tumor.

People who have two mutated copies of the BRCA2 gene have one type of Fanconi anemia. This condition is caused by extremely reduced levels of the BRCA2 protein in cells, which allows the accumulation of damaged DNA. Patients with Fanconi anemia are prone to several types of leukemia (a type of blood cell cancer); solid tumors, particularly of the head, neck, skin, and reproductive organs; and bone marrow suppression (reduced blood cell production that leads to anemia). Women having inherited a defective BRCA1 or BRCA2 gene have risks for breast and ovarian cancer that are so high and seem so selective that many mutation carriers choose to have prophylactic surgery. There has been much conjecture to explain such apparently striking tissue specificity. Major determinants of where BRCA1 and BRCA2 associated hereditary cancers occur are related to tissue specificity of the cancer pathogen, the agent that causes chronic inflammation or the carcinogen. The target tissue may have receptors for the pathogen, become selectively exposed to carcinogens and an infectious process. An innate genomic deficit impairs normal responses and exacerbates the susceptibility to disease in organ targets. This theory also fits data for several tumor suppressors beyond BRCA1 or BRCA2. A major advantage of this model is that it suggests there are some options in addition to prophylactic surgery.[28]

In addition to breast cancer in men and women, mutations in BRCA2 also lead to an increased risk of ovarian, Fallopian tube, prostate, and pancreatic cancers, as well as malignant melanoma. In some studies, mutations in the central part of the gene have been associated with a higher risk of ovarian cancer and a lower risk of prostate cancer than mutations in other parts of the gene. Several other types of cancer have also been seen in certain families with BRCA2 mutations.

In general, strongly inherited gene mutations (including mutations in BRCA2) account for only 5-10% of breast cancer cases; the specific risk of getting breast or other cancer for anyone carrying a BRCA2 mutation depends on many factors.[29]

History

The BRCA2 gene was discovered in 1994 by Professor Michael Stratton along with 39 coauthor scientists[30] (Institute of Cancer Research, UK).[10][31] Scientists from several institutions, including the Wellcome Trust Sanger Institute (Hinxton, Cambs, UK) collaborated with Stratton to isolate the gene.

In honour of this discovery and collaboration, the Wellcome Trust participated in the construction of a cycle and foot path between the Addenbrooke's Hospital site in Cambridge and the nearby village of Great Shelford in 2005. The path by Cambridgeshire County Council and Sustrans is decorated with 10,257 stripes of 4 colours representing the nucleotide sequence of BRCA2 (green representing adenine, blue representing cytosine, yellow representing guanine, and red representing thymine).[32] It makes up part of National Cycle Route 11, and can be seen from trains running between Cambridge and London.

Germ line BRCA2 mutations and founder effect

All germ line BRCA2 mutations identified to date have been inherited, suggesting the possibility of a large "founder" effect in which a certain mutation is common to a well-defined population group and can theoretically be traced back to a common ancestor. Given the complexity of mutation screening for BRCA2, these common mutations may simplify the methods required for mutation screening in certain populations. Analysis of mutations that occur with high frequency also permits the study of their clinical expression.[33] A striking example of a founder mutation is found in Iceland, where a single BRCA2 (999del5) mutation accounts for virtually all breast/ovarian cancer families.[34][35] This frame-shift mutation leads to a highly truncated protein product. In a large study examining hundreds of cancer and control individuals, this 999del5 mutation was found in 0.6% of the general population. Of note, while 72% of patients who were found to be carriers had a moderate or strong family history of breast cancer, 28% had little or no family history of the disease. This strongly suggests the presence of modifying genes that affect the phenotypic expression of this mutation, or possibly the interaction of the BRCA2 mutation with environmental factors. Additional examples of founder mutations in BRCA2 are given in the table below.

Population or subgroup BRCA2 mutation(s)[33][36] Reference(s)
Ashkenazi Jewish 6174delT [37]
Dutch 5579insA [38]
Finns 8555T>G, 999del5, IVS23-2A>G [39][40]
French Canadians 8765delAG, 3398delAAAAG [41][42][43]
Hungarians 9326insA [44]
Icelandics 999del5 [34][35]
Italians 8765delAG [45]
Northern Irish 6503delTT [46]
Pakistanis 3337C>T [47]
Scottish 6503delTT [46]
Slovenians IVS16-2A>G [48]
Spanish 3034delAAAC(codon936), 9254del5 [49]
Swedish 4486delG [50]

Meiosis

In the plant Arabidopsis thaliana, loss of the BRCA2 homolog AtBRCA2 causes severe defects in both male meiosis and in the development of the female gametocyte.[51] AtBRCA2 protein is required for proper localization of the synaptonemal complex protein AtZYP1 and the recombinases AtRAD51 and AtDMC1. Furthermore, AtBRCA2 is required for proper meiotic synapsis. Thus AtBRCA2 is likely important for meiotic recombination. It appears that AtBRCA2 acts during meiosis to control the single-strand invasion steps mediated by AtRAD51 and AtDMC1 occurring during meiotic homologous recombinational repair of DNA damages.[51]

Homologs of BRCA2 are also essential for meiosis in the fungus Ustilago maydis,[52] the worm Caenorhabditis elegans,[53][54] and the fruitfly Drosophila melanogaster.[55]

Mice that produce truncated versions of BRCA2 are viable but sterile.[56] BRCA2 mutant rats have a phenotype of growth inhibition and sterility in both sexes.[57] Aspermatogenesis in these mutant rats is due to a failure of homologous chromosome synapsis during meiosis.

BRC repeat sequences

DMC1 (DNA meiotic recombinase 1) is a meiosis specific homolog of RAD51 that mediates strand exchange during homologous recombinational repair. DMC1 promotes the formation of DNA strand invasion products (joint molecules) between homologous DNA molecules. Human DMC1 interacts directly with each of a series of repeat sequences in the BRCA2 protein (called BRC repeats) that stimulate joint molecule formation by DMC1.[58] BRC repeats conform to a motif consisting of a sequence of about 35 highly conserved amino acids that are present at least once in all BRCA2-like proteins. The BRCA2 BRC repeats stimulate joint molecule formation by promoting the interaction of single-stranded DNA (ssDNA) with DMC1.[58] The ssDNA complexed with DMC1 can pair with homologous ssDNA from another chromosome during the synapsis stage of meiosis to form a joint molecule, a central step in homologous recombination. Thus the BRC repeat sequences of BRCA2 appear to play a key role in recombinational repair of DNA damages during meiotic recombination.

Overall, it appears that homologous recombination during meiosis functions to repair DNA damages,[59] and that BRCA2 plays a key role in performing this function.

Neurogenesis

BRCA2 is required in the mouse for neurogenesis and suppression of medulloblastoma.[60] ‘’BRCA2’’ loss profoundly affects neurogenesis, particularly during embryonic and postnatal neural development. These neurological defects arise from DNA damage.[60]

Epigenetic control of BRCA2

Epigenetic alterations in expression of BRCA2 (causing over-expression or under-expression) are very frequent in sporadic cancers (see Table below) while mutations in BRCA2 are rarely found.[61][62][63]

In non-small cell lung cancer, BRCA2 is epigenetically repressed by hypermethylation of the promoter.[64] In this case, promoter hypermethylation is significantly associated with low mRNA expression and low protein expression but not with loss of heterozygosity of the gene.

In sporadic ovarian cancer, an opposite effect is found. BRCA2 promoter and 5'-UTR regions have relatively few or no methylated CpG dinucleotides in the tumor DNA compared with that of non-tumor DNA, and a significant correlation is found between hypomethylation and a >3-fold over-expression of BRCA2.[65] This indicates that hypomethylation of the BRCA2 promoter and 5'-UTR regions leads to over-expression of BRCA2 mRNA.

One report indicated some epigenetic control of BRCA2 expression by the microRNAs miR-146a and miR-148a.[66]

BRCA2 expression in cancer

In eukaryotes, BRCA2 protein has an important role in homologous recombinational repair. In mice and humans, BRCA2 primarily mediates orderly assembly of RAD51 on single-stranded (ss) DNA, the form that is active for homologous pairing and strand invasion.[67] BRCA2 also redirects RAD51 from double-stranded DNA and prevents dissociation from ssDNA.[67] In addition, the four paralogs of RAD51, consisting of RAD51B (RAD51L1), RAD51C (RAD51L2), RAD51D (RAD51L3), XRCC2 form a complex called the BCDX2 complex (see Figure: Recombinational repair of DNA). This complex participates in RAD51 recruitment or stabilization at damage sites.[25] The BCDX2 complex appears to act by facilitating the assembly or stability of the RAD51 nucleoprotein filament. RAD51 catalyses strand transfer between a broken sequence and its undamaged homologue to allow re-synthesis of the damaged region (see homologous recombination models).

Some studies of cancers report over-expressed BRCA2 whereas other studies report under-expression of BRCA2. At least two reports found over-expression in some sporadic breast tumors and under-expression in other sporadic breast tumors.[68][69] (see Table).

Many cancers have epigenetic deficiencies in various DNA repair genes (see Frequencies of epimutations in DNA repair genes in cancers). These repair deficiencies likely cause increased unrepaired DNA damages. The over-expression of BRCA2 seen in many cancers may reflect compensatory BRCA2 over-expression and increased homologous recombinational repair to at least partially deal with such excess DNA damages. Egawa et al.[70] suggest that increased expression of BRCA2 can be explained by the genomic instability frequently seen in cancers, which induces BRCA2 mRNA expression due to an increased need of BRCA2 for DNA repair.

Under-expression of BRCA2 would itself lead to increased unrepaired DNA damages. Replication errors past these damages (see translesion synthesis) would lead to increased mutations and cancer.

BRCA2 expression in sporadic cancers
Cancer Over or Under expression Frequency of altered expression Evaluation method Ref.
Sporadic ovarian cancer Over-expression 80% messenger RNA [65]
Sporadic ovarian cancer Under-expression 42% immunohistochemistry [71]
(recurrent cancer in study above) Increased-expression 71% immunohistochemistry [71]
Non-small cell lung cancer Under-expression 34% immunohistochemistry [64]
Breast cancer Over-expression 66% messenger RNA [70]
Breast cancer Over-expression 20% messenger RNA [68]
(same study as above) Under-expression 11% messenger RNA [68]
Breast cancer Over-expression 30% immunohistochemistry [69]
(same study as above) Under-expression 30% immunohistochemistry [69]
Triple negative breast cancer Under-expression 90% immunohistochemistry [72]

Interactions

BRCA2 has been shown to interact with

Domain architecture

BRCA2 contains a number of 39 amino acid repeats that are critical for binding to RAD51 (a key protein in DNA recombinational repair) and resistance to methyl methanesulphonate treatment.[89][96][97][105]

The BRCA2 helical domain adopts a helical structure, consisting of a four-helix cluster core (alpha 1, alpha 8, alpha 9, alpha 10) and two successive beta-hairpins (beta 1 to beta 4). An approximately 50-amino acid segment that contains four short helices (alpha 2 to alpha 4), meanders around the surface of the core structure. In BRCA2, the alpha 9 and alpha 10 helices pack with the BRCA2 OB1 domain through van der Waals contacts involving hydrophobic and aromatic residues, and also through side-chain and backbone hydrogen bonds. This domain binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome.[103]

The BRCA OB1 domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein.[103]

The BRCA OB3 domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding.[103]

The Tower domain adopts a secondary structure consisting of a pair of long, antiparallel alpha-helices (the stem) that support a three-helix bundle (3HB) at their end. The 3HB contains a helix-turn-helix motif and is similar to the DNA binding domains of the bacterial site-specific recombinases, and of eukaryotic Myb and homeodomain transcription factors. The Tower domain has an important role in the tumour suppressor function of BRCA2, and is essential for appropriate binding of BRCA2 to DNA.[103]

Patents, enforcement, litigation, and controversy

A patent application for the isolated BRCA1 gene and cancer-cancer promoting mutations, as well as methods to diagnose the likelihood of getting breast cancer, was filed by the University of Utah, National Institute of Environmental Health Sciences (NIEHS) and Myriad Genetics in 1994;[15] over the next year, Myriad, in collaboration with other investigators, isolated and sequenced the BRCA2 gene and identified relevant mutations, and the first BRCA2 patent was filed in the U.S. by Myriad and the other institutions in 1995.[14] Myriad is the exclusive licensee of these patents and has enforced them in the US against clinical diagnostic labs.[18] This business model led from Myriad being a startup in 1994 to being a publicly traded company with 1200 employees and about $500M in annual revenue in 2012;[17] it also led to controversy over high prices and the inability to get second opinions from other diagnostic labs, which in turn led to the landmark Association for Molecular Pathology v. Myriad Genetics lawsuit.[18][106] The patents begin to expire in 2014.

According to an article published in the journal, Genetic Medicine, in 2010,[107] "The patent story outside the United States is more complicated.... For example, patents have been obtained but the patents are being ignored by provincial health systems in Canada. In Australia and the UK, Myriad's licensee permitted use by health systems, but announced a change of plans in August 2008. ... Only a single mutation has been patented in Myriad's lone European-wide patent, although some patents remain under review of an opposition proceeding. In effect, the United States is the only jurisdiction where Myriad's strong patent position has conferred sole-provide status."[107][108] Peter Meldrum, CEO of Myriad Genetics, has acknowledged that Myriad has "other competitive advantages that may make such [patent] enforcement unnecessary" in Europe.[109]

Legal decisions surrounding the BRCA1 and BRCA2 patents will affect the field of genetic testing in general.[110] In June 2013, in Association for Molecular Pathology v. Myriad Genetics (No. 12-398), the US Supreme Court unanimously ruled that, "A naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated," invalidating Myriad's patents on the BRCA1 and BRCA2 genes. However, the Court also held that manipulation of a gene to create something not found in nature could still be eligible for patent protection.[111] The Federal Court of Australia came to the opposite conclusion, upholding the validity of an Australian Myriad Genetics patent over the BRCA1 gene in February 2013,[112] but this decision is being appealed and the appeal will include consideration of the US Supreme Court ruling.[113]

See also

References

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  32. ^ Route information board
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Further reading

External links

This article incorporates text from the public domain Pfam and InterPro IPR002093

This article incorporates text from the public domain Pfam and InterPro IPR015252

This article incorporates text from the public domain Pfam and InterPro IPR015187

This article incorporates text from the public domain Pfam and InterPro IPR015205

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.

BRCA2 repeat Provide feedback

The alignment covers only the most conserved region of the repeat.

Literature references

  1. Bork P, Blomberg N, Nilges M; , Nat Genet 1996;13:22-23.: Internal repeats in the BRCA2 protein sequence. PUBMED:8673099 EPMC:8673099


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002093

The breast cancer type 2 susceptibility protein has a number of 39 amino acid repeats [PUBMED:8673099] that are critical for binding to RAD51 (a key protein in DNA recombinational repair) and resistance to methyl methanesulphonate treatment [PUBMED:9405383, PUBMED:9560268, PUBMED:9811893]. BRCA2 is a breast tumour suppressor with a potential function in the cellular response to DNA damage. At the cellular level, expression is regulated in a cell-cycle dependent manner and peak expression of BRCA2 mRNA is found in S phase, suggesting BRCA2 may participate in regulating cell proliferation. There are eight repeats in BRCA2 designated as BRC1 to BRC8. BRC1, BRC2, BRC3, BRC4, BRC7, and BRC8 are highly conserved and bind to Rad51, whereas BRC5 and BRC6 are less well conserved and do not bind to Rad51 [PUBMED:10551859]. It has been suggested that BRCA2 plays a role in positioning Rad51 at the site of DNA repair or in removing Rad51 from DNA once repair has been completed.

Domain organisation

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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 (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...

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
(61)
Full
(1069)
Representative proteomes UniProt
(3087)
NCBI
(4606)
Meta
(0)
RP15
(242)
RP35
(543)
RP55
(845)
RP75
(1047)
Jalview View  View  View  View  View  View  View  View   
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(61)
Full
(1069)
Representative proteomes UniProt
(3087)
NCBI
(4606)
Meta
(0)
RP15
(242)
RP35
(543)
RP55
(845)
RP75
(1047)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(61)
Full
(1069)
Representative proteomes UniProt
(3087)
NCBI
(4606)
Meta
(0)
RP15
(242)
RP35
(543)
RP55
(845)
RP75
(1047)
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.

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: Prosite
Previous IDs: BRCA2_repeat;
Type: Family
Author: Bateman A
Number in seed: 61
Number in full: 1069
Average length of the domain: 30.90 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 8.17 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 19.9 20.2
Model length: 33
Family (HMM) version: 16
Download: download the raw HMM for this family

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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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.

Interactions

There is 1 interaction for this family. More...

Rad51

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 BRCA2 domain has been found. There are 1 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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