Recombinase A: Difference between revisions

[[Recombinase A]] (RecA), a naturally aggregating 352 amino acid protein involved in DNA repair, is an important asset to the genetic integrity of the ''Escherichia coli'' (''E. coli'') genome.<ref name=Shan> Shan, Q.; Cox, M. M.; Inman, R. B. DNA Strand Exchange Promoted by RecA K72R. J. Biol. Chem. 1996, 271, 5712-5724. DOI:10.1074/jbc.271.10.5712 </ref> The survival of all species rely on such DNA repair processes. RecA homologues are found in all kingdoms including archaebacteria, eubacteria, and eukaryotes.<ref name=Brendel> Brendel, V.; Brocchieri, L.; Sandler, S.J.; Clark, A.J.; Karlin, S. Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J. Mol. Evol. 1997, 44, 528-541. DOI: 10.1007/PL00006177 </ref> RAD51, for example, is a RecA homologue found specifically in humans.<ref name=Baumann> Baumann, P.; Benson, F. E.; West, S. C. Human Rad51 Protein Promotes ATP-Dependent Homologous Pairing and Strand Transfer Reactions in Vitro. Cell. 1996, 87, 757-766. DOI: 10.1016/S0092-8674(00)81394-X </ref>  An over-expression of RAD51 in the nuclei of tumor cells when compared to those of normal breast tissue has been linked to sporadic, non-hereditary, breast cancers.<ref name=Maacke> Maacke, H.; Opitz, S.; Jost, K.; Hamdorf, W.; Henning, W. Krüger, S. Feller, A.C.; Lopens, A.; Diedrich, K.; Schwinger, E.; Stürzbecher, H.W. Over-expression of wild-type Rad51 correlates with histological grading of invasive ductal breast cancer. Int. J. Cancer. 2000, 88, 907-913. DOI: 10.1002/1097-0215(20001215)88:63.0.CO;2-4 </ref>

In ''E. coli'', RecA’s central function involves strand exchange, specifically recombinational DNA repair.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> The DNA recombination mechanism for RecA is a process that results in the exchange of strands between two homologous DNA molecules.<ref name=Nayak> Nayak, S.; Hildebrand, E.L.; Bryant, F.R. ADP-dependent DNA strand exchange by the Mutant RecA protein. J. Biol. Chem.2001, 276, 14933-14938. DOI:10.1074/jbc.M100470200 </ref> The DNA that results from this process is a nicked circular dsDNA molecule and one or two linear ssDNA molecules, depending on the number of DNA strands involved (three or four).<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> <ref name=Nayak> Nayak, S.; Hildebrand, E.L.; Bryant, F.R. ADP-dependent DNA strand exchange by the Mutant RecA protein. J. Biol. Chem.2001, 276, 14933-14938. DOI:10.1074/jbc.M100470200 </ref> During DNA strand exchange, adenosine triphosphate (ATP) is hydrolyzed to form adenosine diphosphate (ADP) and inorganic phosphate (Pi). ATP hydrolysis is required for DNA strand exchange to be unidirectional (without ATP hydrolysis, strand exchange is also bidirectional), for the circumvention of various structural obstacles on the DNA molecule such as heterologous inserts, and for DNA strand exchange to occur with four stands of DNA.<ref name=Shan> Shan, Q.; Cox, M. M.; Inman, R. B. DNA Strand Exchange Promoted by RecA K72R. J. Biol. Chem. 1996, 271, 5712-5724. DOI:10.1074/jbc.271.10.5712 </ref> <ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref>

RecA is also involved in inducing the SOS response to DNA damage by assisting in the cleavage, and consequent inactivation, of proteins.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> Examples of such proteins are the LexA repressor and the λ repressor.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref>  

As RecA has many different functions, it also has several different binding sites for DNA, ATP, the LexA repressor, the λ repressor, as well as other RecA protein monomers to form a variety of oligomers.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> <ref name=Story> Story, R. M.; Weber, I. T.; Steitz, T. A. The structure of the E. coli recA protein monomer and polymer. Nature (London) 1992, 355, 318-325. DOI: 10.1038/355318a0 </ref> <ref name=Walker> Walker, J. E.; Saraste, M.; Runswick, M. J. Gay, N. J. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982, 1, 945-951. PMCID: PMC553140 </ref> There are six RecA proteins per turn of the helix, and each individual monomer is capable of binding three base pairs of the extended conformation of DNA.T10  This filament is not the only oligomer of RecA that exists in solution, however. Sattin and Goh have reported a variety of RecA structures in buffer, such as monomers, hexamers, rods/fibrils, protofibrils (essentially fibrils with a narrower diameter), and other small aggregates.K11 Moreover, the type and amount of these different aggregation states is dynamic. Brenner and Zlotnick reported that the presence of monovalent salts changed the distribution of RecA aggregation states and that higher protein concentration tended to correspond to more aggregated structures.K10  ATP hydrolysis occurs in the region of a loop consisting of amino acids 66-73 of the protein. This loop, which corresponds to the Walker A box motif, has the sequence GPESSGKT.K6,K8 This sequence corresponds to a variation known as the phosphate binding loop, which has a sequence [G/A]XXXXGK[T/S] found in many nucleoside triphosphate (NTP)-binding proteins.K8,K9 Several of the residues in this phosphate binding loop can be seen interacting with the β and γ phosphates of ATP in the ATP-binding site proposed by Story and Steitz.K8 The binding of various ligands to RecA has been shown to change the pitch, the “distance covered by each turn of the helix,” of the protein filament.k13 RecA in the absence of any cofactor is in a “closed” conformation with a helical pitch of 7 nm (DNA binding to the RecA does not alter the pitch significantly). RecA bound to ATP increases the pitch to 9 nm.k14 This RecA-ATP structure is marked by a higher affinity for DNA.k6,k15 However, the binding of ADP to RecA only raises the pitch to 8.2 nm,k14 the conformation of which is known to have a lower affinity for DNA.k6,k15