Literature summary for 3.6.4.B7 extracted from

Cooper, D.; Lovett, S.
Recombinational branch migration by the RadA/Sms paralog of RecA in Escherichia coli (2016), eLife, 5, e10807 .

Search for more literature for 3.6.4.B7

Activating Compound

Activating Compound	Comment	Organism	Structure
ADP	activates binding of ssDNA	Escherichia coli
additional information	no DNA binding is detected in the absence of nucleotide (ADP), but also no DNA binding is detected with ATP or dATP or in the presence of poorly-hydrolyzable ATP analogues, ATPgammaS or AMP-PNP	Escherichia coli
RecA	RecA is required for RadA-stimulation of strand exchange. RecA can also catalyze strand-exchange between two duplex molecules, provided that strand exchange is initiated at a short ssDNA gap in the substrate. These reactions produce full 4-strand Holliday junction intermediates	Escherichia coli
single-stranded DNA	ssDNA, like RecA, RadA's ATPase activity is strongly stimulated by ssDNA	Escherichia coli

Protein Variants

Protein Variants	Comment	Organism
C28Y	RadA mutant C28Y retains the ATPase activity but is defective in DNA binding	Escherichia coli
K108R	the mutation at the Walker A sequence results in a dominant-negative RadA allele in Escherichia coli, it shows highly reduced DNA binding compared to wild-type	Escherichia coli
K258A	the mutation in the KNRFG motif negates RadA function and is partially dominant in vivo, it shows highly reduced DNA binding compared to wild-type	Escherichia coli
additional information	mutation of serine 372 of RadA, comparable in alignments to the active site serine of Lon, does not affect RadA genetic function and this serine is not conserved among RadAs	Escherichia coli
S372A	the RadA mutant retains ATPase and DNA-binding activities similar to wild-type	Escherichia coli

Inhibitors

Inhibitors	Comment	Organism	Structure
additional information	binding of poly(dT)30 is inhibited if poly(dA)30 is allowed to anneal to the substrate, showing that RadA binds more poorly to duplex DNA	Escherichia coli

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
ATP + H2O	Escherichia coli	-	ADP + phosphate	-	?

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	P24554	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
ATP + H2O	-	Escherichia coli	ADP + phosphate	-	?
additional information	an NADH-coupled assay is used to measure the ATPase activity of RadA, in the presence or absence of various DNA cofactors, circular ssDNA (jX174 virion) and dsDNA (jX174 RF DNA). DNA substrate specificity of RadA binding, overview. The wild-type RadA protein preferentially binds single-strand DNA in the presence of ADP. Binding preference for by poly(dT) by RadA and also by RecA. RadA is observed to bind poly(dT)30 when flanked on both 5' and 3' ends by 30 nucleotides of natural DNA sequence. Catalysis of RecA-mediated strand-exchange reactions between 5386 nucleotide circular jX174 ssDNA and linear duplex DNA in the presence of ATP and an ATP-regeneration system, ATP hydrolysis in reactions including RecA, SSB and RadA	Escherichia coli	?	-	-

Subunits

Subunits	Comment	Organism
More	RadA is a 460 amino acid protein that has three well-conserved domains also found in other proteins, as well as a 5-amino acid motif highly conserved among radA orthologs. The N-terminal 30 amino acids form a putative zinc-finger domain with a C4 motif, CXXC-Xn-CXXC	Escherichia coli

Synonyms

Synonyms	Comment	Organism
RadA/Sms	-	Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Escherichia coli

General Information

General Information	Comment	Organism
malfunction	loss of radA, by itself, reduces recovery of genetic rearrangements at tandem-repeated sequences, which are promoted by defects in the replication fork helicase, DnaB. In addition, loss of RadA reduces homologous recombination when in combination with loss of RuvAB or RecG as measured by conjugation with Hfr donors (RuvAB and RecG are DNA motor proteins that branch-migrate recombination intermediates such as Holliday junctions during the late stages of homologous recombination). Mutations in the Walker A, KNRFG and zinc finger motifs abolish RadA's branch migration activity in RecA-coupled reactions and lead to the accumulation of strand exchange intermediate species	Escherichia coli
additional information	RadA is a 460 amino acid protein that has three well-conserved domains also found in other proteins, as well as a 5-amino acid motif highly conserved among radA orthologs. The N-terminal 30 amino acids form a putative zinc-finger domain with a C4 motif, CXXC-Xn-CXXC	Escherichia coli
physiological function	RadA can bind to single-stranded DNA and stimulate branch migration to increase the rate of homologous recombination. RadA allows branch migration to occur even when RecA is missing, but RadA is unable to begin strand exchange if RecA is not present. The process of branch migration stabilizes the DNA molecules during homologous recombination and may also allow the repaired DNA strand to engage the machinery that copies DNA. In vitro RecA mediates strand exchange, a key step of recombination. RadA has an effect on the structure of RecA. The wild-type RadA protein preferentially binds single-strand DNA in the presence of ADP, exhibits ATPase activity stimulated by DNA, and increases the rate of RecA-mediated recombination in vitro by stimulation of branch migration. Branch migration can be mediated by RadA even in the absence of RecA and is highly directional in nature, with preferential extension of the heteroduplex in the 5' to 3' direction, relative to the initiating single-strand, this is codirectional with that of RecA-mediated strand exchange. DNA branch migration and exchange mechanism, overview	Escherichia coli

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Release 2023.1 (January 2023)