DNA Repair and Replication: 69 (Advances in Protein Chemistry)

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Volume 73. Fibrous Proteins: Amyloids, Prions and Beta Proteins

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:. 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. There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary. The tree is built by looking at each sequence in the full alignment for the family. 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.

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.

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.

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 are 7 interactions for this family. We determine these interactions using i Pfam , 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 i Pfam algorithm in the journal article that accompanies the website.

There are 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. Comments or questions on the site? Send a mail to pfam-help ebi. Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.

Loading page components …. Summary: DNA polymerase family A. Does Pfam agree with the content of the Wikipedia entry? Editing Wikipedia articles Before you edit for the first time Wikipedia is a free, online encyclopedia. You should take a few minutes to view the following pages: Five pillars Policies and quidelines Wikipedia help contents Wikipedia Tips Editing help How your contribution will be recorded Anyone can edit a Wikipedia entry. Contact us The community annotation is a new facility of the Pfam web site.

Further information: DNA polymerase nu. The Journal of Biological Chemistry. Deoxy- ribonucleic acid polymerase in spores of Bacillus subtilis". Preparation of substrates and partial purification of an enzyme from Escherichia coli". Further purification and properties of deoxyribonucleic acid polymerase of Escherichia coli". Synthesis of a polymer of deoxyadenylate and deoxythymidylate". Nobel Foundation. Retrieved December 1, Retrieved April 4, Mary Finch. Bibcode : Natur. Molecular biology of the gene 6th ed. Journal of Molecular Biology. World Scientific Publishing Company. Cell Cycle.

Molecular Microbiology. The chi psi complex functions by increasing the affinity of tau and gamma for delta.

Summary: DNA polymerase family A

Retrieved Annual Review of Biochemistry. Critical Reviews in Biochemistry and Molecular Biology. Bibcode : PNAS Biochimica et Biophysica Acta. Marks' Basic Medical Biochemistry: a clinical approach 4th ed. Molecular Cell. Molecular and Cellular Biology. Advances in Protein Chemistry and Structural Biology.

Cell Research. Cellular and Molecular Life Sciences. Nucleic Acids Research. DNA replication comparing Prokaryotic to Eukaryotic.

Movement: Processivity DNA ligase. Transferases : phosphorus -containing groups EC 2. Phosphoglycerate Aspartate kinase. Ribose-phosphate diphosphokinase Thiamine diphosphokinase. UTP—glucosephosphate uridylyltransferase Galactosephosphate uridylyltransferase. Recombinase Integrase Transposase. N-acetylglucosaminephosphate transferase. Protein-histidine pros-kinase Protein-histidine tele-kinase Histidine kinase. Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator. EC number Enzyme superfamily Enzyme family List of enzymes.

Molecular and Cellular Biology portal. Each row contains the following information: the number of sequences which exhibit this architecture a textual description of the architecture, e. Gla, EGF x 2, Trypsin.

Department of Chemistry

Senescence in cells may serve as a functional alternative to apoptosis in cases where the physical presence of a cell for spatial reasons is required by the organism, [13] which serves as a "last resort" mechanism to prevent a cell with damaged DNA from replicating inappropriately in the absence of pro-growth cellular signaling. Unregulated cell division can lead to the formation of a tumor see cancer , which is potentially lethal to an organism.

Therefore, the induction of senescence and apoptosis is considered to be part of a strategy of protection against cancer. DNA damage and mutation are fundamentally different. Damage results in physical abnormalities in the DNA, such as single- and double-strand breaks, 8-hydroxydeoxyguanosine residues, and polycyclic aromatic hydrocarbon adducts. DNA damage can be recognized by enzymes, and thus can be correctly repaired if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying.

If a cell retains DNA damage, transcription of a gene can be prevented, and thus translation into a protein will also be blocked. Replication may also be blocked or the cell may die. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired. At the cellular level, mutations can cause alterations in protein function and regulation. Mutations are replicated when the cell replicates. In a population of cells, mutant cells will increase or decrease in frequency according to the effects of the mutation on the ability of the cell to survive and reproduce.

Although distinctly different from each other, DNA damage and mutation are related because DNA damage often causes errors of DNA synthesis during replication or repair; these errors are a major source of mutation. Given these properties of DNA damage and mutation, it can be seen that DNA damage is a special problem in non-dividing or slowly-dividing cells, where unrepaired damage will tend to accumulate over time. On the other hand, in rapidly-dividing cells, unrepaired DNA damage that does not kill the cell by blocking replication will tend to cause replication errors and thus mutation. The great majority of mutations that are not neutral in their effect are deleterious to a cell's survival.

Thus, in a population of cells composing a tissue with replicating cells, mutant cells will tend to be lost. However, infrequent mutations that provide a survival advantage will tend to clonally expand at the expense of neighboring cells in the tissue.

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This advantage to the cell is disadvantageous to the whole organism, because such mutant cells can give rise to cancer. Thus, DNA damage in frequently dividing cells, because it gives rise to mutations, is a prominent cause of cancer. In contrast, DNA damage in infrequently-dividing cells is likely a prominent cause of aging. Cells cannot function if DNA damage corrupts the integrity and accessibility of essential information in the genome but cells remain superficially functional when non-essential genes are missing or damaged.

Depending on the type of damage inflicted on the DNA's double helical structure, a variety of repair strategies have evolved to restore lost information. If possible, cells use the unmodified complementary strand of the DNA or the sister chromatid as a template to recover the original information.

Without access to a template, cells use an error-prone recovery mechanism known as translesion synthesis as a last resort. Damage to DNA alters the spatial configuration of the helix, and such alterations can be detected by the cell. Once damage is localized, specific DNA repair molecules bind at or near the site of damage, inducing other molecules to bind and form a complex that enables the actual repair to take place. Cells are known to eliminate three types of damage to their DNA by chemically reversing it. These mechanisms do not require a template, since the types of damage they counteract can occur in only one of the four bases.

Such direct reversal mechanisms are specific to the type of damage incurred and do not involve breakage of the phosphodiester backbone. The formation of pyrimidine dimers upon irradiation with UV light results in an abnormal covalent bond between adjacent pyrimidine bases. Another type of damage, methylation of guanine bases, is directly reversed by the protein methyl guanine methyl transferase MGMT , the bacterial equivalent of which is called ogt. This is an expensive process because each MGMT molecule can be used only once; that is, the reaction is stoichiometric rather than catalytic.

Most of the difference between the two values is accounted for by the 3' to 5' exonuclease proofreading activity of the DNA polymerase in both bacteria and eukaryotes. When an incorrect nucleotide is inserted, the polymerase detects the mismatched base pairs and corrects the area by back spacing to remove the wrong nucleotide and then resuming synthesis in the forward directions.

The mutator mutations in E. Mutator mutants have much higher than normal mutation frequency for all genes. These mutants have mutations in genes for proteins whose normal functions are required for accurate DNA replication. For example mut D mutator gene of E. The mut D mutants are defective in 3' to 5' proofreading activity, so that many incorrectly inserted nucleotide are left unrepaired. Photo reactivation occurs when an enzyme called photolyase is activated by a photon of light and splits the dimmers apart. Photolyase has been found in bacteria and in simple eukaryotes but not in humans.

Alkylating agents transfer alkyl groups usually methyl or ethyl groups onto the bases. The mutagen MMS methylates the oxygen of carbon 6 in guanine. This enzyme remove methyl group from guanine thereby changing the base back ti its original form. Similar specific system exist to repair alkylated thymine. Mutations of the genes encoding this repair enzymes results in a much higher rate of spontaneous mutation.

Dispite prrofreading of DNA polymerase, a number of mismatched base pair remain uncorrected after replication has been completed. In the next round of replication this errors will become fixed as mutations if they are not repaired. This system recognizes mismatched base pairs, excises the incorrect bases, and then carry out repair synthesis. When only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand.

In order to repair damage to one of the two paired molecules of DNA, there exist a number of excision repair mechanisms that remove the damaged nucleotide and replace it with an undamaged nucleotide complementary to that found in the undamaged DNA strand. Double-strand breaks, in which both strands in the double helix are severed, are particularly hazardous to the cell because they can lead to genome rearrangements. It was noted in some studies that double-strand breaks and a "cross-linkage joining both strands at the same point is irreparable because neither strand can then serve as a template for repair.

The cell will die in the next mitosis or in some rare instances, mutate. If these overhangs are compatible, repair is usually accurate. Loss of damaged nucleotides at the break site can lead to deletions, and joining of nonmatching termini forms insertions or translocations. NHEJ is especially important before the cell has replicated its DNA, since there is no template available for repair by homologous recombination. There are "backup" NHEJ pathways in higher eukaryotes. Homologous recombination requires the presence of an identical or nearly identical sequence to be used as a template for repair of the break.

The enzymatic machinery responsible for this repair process is nearly identical to the machinery responsible for chromosomal crossover during meiosis. This pathway allows a damaged chromosome to be repaired using a sister chromatid available in G2 after DNA replication or a homologous chromosome as a template. DSBs caused by the replication machinery attempting to synthesize across a single-strand break or unrepaired lesion cause collapse of the replication fork and are typically repaired by recombination. MMEJ starts with short-range end resection by MRE11 nuclease on either side of a double-strand break to reveal microhomology regions.

There is pairing of microhomology regions followed by recruitment of flap structure-specific endonuclease 1 FEN1 to remove overhanging flaps. The extremophile Deinococcus radiodurans has a remarkable ability to survive DNA damage from ionizing radiation and other sources. Partially overlapping fragments are then used for synthesis of homologous regions through a moving D-loop that can continue extension until they find complementary partner strands.

In the final step there is crossover by means of RecA -dependent homologous recombination. Topoisomerases introduce both single- and double-strand breaks in the course of changing the DNA's state of supercoiling , which is especially common in regions near an open replication fork. Such breaks are not considered DNA damage because they are a natural intermediate in the topoisomerase biochemical mechanism and are immediately repaired by the enzymes that created them.

DNA polymerase IV or V, from the Y Polymerase family , often with larger active sites that can facilitate the insertion of bases opposite damaged nucleotides. The polymerase switching is thought to be mediated by, among other factors, the post-translational modification of the replication processivity factor PCNA.

Translesion synthesis polymerases often have low fidelity high propensity to insert wrong bases on undamaged templates relative to regular polymerases. However, many are extremely efficient at inserting correct bases opposite specific types of damage. From a cellular perspective, risking the introduction of point mutations during translesion synthesis may be preferable to resorting to more drastic mechanisms of DNA repair, which may cause gross chromosomal aberrations or cell death.

In short, the process involves specialized polymerases either bypassing or repairing lesions at locations of stalled DNA replication. For example, Human DNA polymerase eta can bypass complex DNA lesions like guanine-thymine intra-strand crosslink, G[8,5-Me]T, although it can cause targeted and semi-targeted mutations. Cells exposed to ionizing radiation , ultraviolet light or chemicals are prone to acquire multiple sites of bulky DNA lesions and double-strand breaks.

The accumulation of damage, to be specific, double-strand breaks or adducts stalling the replication forks , are among known stimulation signals for a global response to DNA damage. The common features of global response are induction of multiple genes , cell cycle arrest, and inhibition of cell division. The packaging of eukaryotic DNA into chromatin presents a barrier to all DNA-based processes that require recruitment of enzymes to their sites of action.

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To allow DNA repair, the chromatin must be remodeled. In eukaryotes, ATP dependent chromatin remodeling complexes and histone-modifying enzymes are two predominant factors employed to accomplish this remodeling process.

Chromatin relaxation occurs rapidly at the site of a DNA damage. This relaxation allows other proteins in the nucleotide excision repair pathway to enter the chromatin and repair UV-induced cyclobutane pyrimidine dimer damages. After rapid chromatin remodeling , cell cycle checkpoints are activated to allow DNA repair to occur before the cell cycle progresses. This is followed by phosphorylation of the cell cycle checkpoint protein Chk1 , initiating its function, about 10 minutes after DNA is damaged. After DNA damage, cell cycle checkpoints are activated.

Checkpoint activation pauses the cell cycle and gives the cell time to repair the damage before continuing to divide. An intra- S checkpoint also exists. These kinases phosphorylate downstream targets in a signal transduction cascade, eventually leading to cell cycle arrest. DNA damage checkpoint is a signal transduction pathway that blocks cell cycle progression in G1, G2 and metaphase and slows down the rate of S phase progression when DNA is damaged. It leads to a pause in cell cycle allowing the cell time to repair the damage before continuing to divide.

Central to all DNA damage induced checkpoints responses is a pair of large protein kinases belonging to the first group of PI3K-like protein kinases-the ATM Ataxia telangiectasia mutated and ATR Ataxia- and Rad-related kinases, whose sequence and functions have been well conserved in evolution. The LexA homodimer is a transcriptional repressor that binds to operator sequences commonly referred to as SOS boxes.

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In Escherichia coli it is known that LexA regulates transcription of approximately 48 genes including the lexA and recA genes. The loss of LexA repressor induces transcription of the SOS genes and allows for further signal induction, inhibition of cell division and an increase in levels of proteins responsible for damage processing. In Escherichia coli , SOS boxes are nucleotide long sequences near promoters with palindromic structure and a high degree of sequence conservation. In other classes and phyla, the sequence of SOS boxes varies considerably, with different length and composition, but it is always highly conserved and one of the strongest short signals in the genome.

The lesion repair genes are induced at the beginning of SOS response. Eukaryotic cells exposed to DNA damaging agents also activate important defensive pathways by inducing multiple proteins involved in DNA repair, cell cycle checkpoint control, protein trafficking and degradation. Such genome wide transcriptional response is very complex and tightly regulated, thus allowing coordinated global response to damage.

Exposure of yeast Saccharomyces cerevisiae to DNA damaging agents results in overlapping but distinct transcriptional profiles. Similarities to environmental shock response indicates that a general global stress response pathway exist at the level of transcriptional activation. In contrast, different human cell types respond to damage differently indicating an absence of a common global response. The probable explanation for this difference between yeast and human cells may be in the heterogeneity of mammalian cells.

In an animal different types of cells are distributed among different organs that have evolved different sensitivities to DNA damage. In general global response to DNA damage involves expression of multiple genes responsible for postreplication repair , homologous recombination, nucleotide excision repair, DNA damage checkpoint , global transcriptional activation, genes controlling mRNA decay, and many others. A large amount of damage to a cell leaves it with an important decision: undergo apoptosis and die, or survive at the cost of living with a modified genome.

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DNA Repair and Replication: 69 (Advances in Protein Chemistry) DNA Repair and Replication: 69 (Advances in Protein Chemistry)
DNA Repair and Replication: 69 (Advances in Protein Chemistry) DNA Repair and Replication: 69 (Advances in Protein Chemistry)
DNA Repair and Replication: 69 (Advances in Protein Chemistry) DNA Repair and Replication: 69 (Advances in Protein Chemistry)
DNA Repair and Replication: 69 (Advances in Protein Chemistry) DNA Repair and Replication: 69 (Advances in Protein Chemistry)
DNA Repair and Replication: 69 (Advances in Protein Chemistry) DNA Repair and Replication: 69 (Advances in Protein Chemistry)
DNA Repair and Replication: 69 (Advances in Protein Chemistry) DNA Repair and Replication: 69 (Advances in Protein Chemistry)
DNA Repair and Replication: 69 (Advances in Protein Chemistry) DNA Repair and Replication: 69 (Advances in Protein Chemistry)
DNA Repair and Replication: 69 (Advances in Protein Chemistry) DNA Repair and Replication: 69 (Advances in Protein Chemistry)

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