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Replication protein A (RPA) is the major protein that binds to single-stranded DNA (ssDNA) in eukaryotic cells. In vitro, RPA shows a much higher affinity for ssDNA than RNA or double-stranded DNA. RPA is required in replication, recombination and repair processes such as
nucleotide excision repair Nucleotide excision repair is a DNA repair mechanism. DNA damage occurs constantly because of chemicals (e.g. intercalating agents), radiation and other mutagens. Three excision repair pathways exist to repair single stranded DNA damage: Nucleo ...
and
homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may be ...
.  It also plays roles in responding to damaged DNA.


Structure

RPA is a heterotrimer, composed of the subunits RPA1 (RPA70) (70kDa subunit), RPA2 (RPA32) (32kDa subunit) and RPA3 (RPA14) (14kDa subunit). The three RPA subunits contain six OB-folds (oligonucleotide/oligosaccharide binding),with
DNA-binding domains A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA sequence (a recognition sequence) or have a genera ...
(DBD) designated DBDs A-F, that bind RPA to single-stranded DNA. DBDs A, B, C and F are located on RPA1, DBD D is located on RPA2, and DBD E is located on RPA3.  DBDs C, D, and E make up the trimerization core of the protein with
flexible linker In molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs ran ...
regions connecting them all together.  Due to these flexible linker regions RPA is considered highly flexible and this supports the dynamic binding that RPA is able to achieve.  Because of this dynamic binding, RPA is also capable of different conformations that leads to varied numbers of nucleotides that it can engage. DBDs A, B, C and D are the sites that are involved in ssDNA binding.  Protein-protein interactions between RPA and other proteins happen at the N-terminal of RPA1, specifically DBD F, along with the
C-terminal The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain ( protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is ...
of RPA2. Phosphorylation of RPA takes place at the N-terminus of RPA2. RPA shares many features with the
CST complex The CST complex is a cellular multiprotein complex involved in telomere maintenance. In budding yeast (''Saccharomyces cerevisiae''), it is composed of the proteins Cdc13, Stn1, and Ten1; in mammals, it consists of the proteins CTC1, STN1, and TEN1 ...
heterotrimer, although RPA has a more uniform 1:1:1
stoichiometry Stoichiometry refers to the relationship between the quantities of reactants and products before, during, and following chemical reactions. Stoichiometry is founded on the law of conservation of mass where the total mass of the reactants equal ...
.


Functions

During DNA replication, RPA prevents single-stranded DNA (ssDNA) from winding back on itself or from forming secondary structures. It also helps protect the ssDNA from being attacked by
endonucleases Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases ...
. This keeps DNA unwound for the
polymerase A polymerase is an enzyme ( EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand using bas ...
to replicate it. RPA also binds to ssDNA during the initial phase of homologous recombination, an important process in DNA repair and
prophase I Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately r ...
of meiosis. Hypersensitivity to DNA damaging agents can be caused by mutations in the RPA gene. Like its role in DNA replication, this keeps ssDNA from binding to itself (self-complementizing) so that the resulting nucleoprotein filament can then be bound by
Rad51 DNA repair protein RAD51 homolog 1 is a protein encoded by the gene ''RAD51''. The enzyme encoded by this gene is a member of the RAD51 protein family which assists in repair of DNA double strand breaks. RAD51 family members are homologous to th ...
and its cofactors. RPA also binds to DNA during the nucleotide excision repair process. This binding stabilizes the repair complex during the repair process. A bacterial homolog is called
single-strand binding protein Single-strand DNA-binding protein (SSB) is a protein found in ''Escherichia coli'' (''E. coli'') bacteria, that binds to single-stranded regions of deoxyribonucleic acid ( DNA). Single-stranded DNA is produced during all aspects of DNA metabolism: ...
(SSB).


See also

*
Single-stranded binding protein Single-stranded binding proteins (SSBs) are a class of proteins that have been identified in both viruses and organisms from bacteria to humans. Viral SSB Although the overall picture of ''human cytomegalovirus'' (HHV-5) DNA synthesis appears ...
* Replication protein A1 * Replication protein A2 * Replication protein A3


References

{{DNA repair Genetics