I. ATP hydrolysis - The Journal of Biological Chemistry

JBC Papers in Press. Published on February 11, 2002 as Manuscript M109915200

Tombline and Fishel page 1 _____________________________________________________________________________

Biochemical Characterization of the human RAD51 Protein: I. ATP hydrolysis*

Genetics and Molecular Biology Program, Department of Microbiology and Immunology, Kimmel Cancer Center, Thomas Jefferson University, 233 S. 10th St. Philadelphia, PA 19107

running title: Cooperativity of the hRAD51 ATPase key words: ATPase, nucleotide switch, molecular switch,

*this work has been supported by Grant CA56542 ¶ To whom requests for reprints should be addressed: Kimmel Cancer Center BLSB 933, 233 S. 10th St., Philadelphia, PA 19107, Phone: (213) 503-1346; Fax: (215) 923-1098; email: [email protected]

Copyright 2002 by The American Society for Biochemistry and Molecular Biology, Inc.

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Gregory Tombline and Richard Fishel¶


Summary The prototypical bacterial RecA protein promotes recombination/repair by catalyzing strand exchange between homologous DNAs. While the mechanism of strand exchange remains enigmatic, ATP-induced cooperativity between RecA protomers is critical for its function. A human RecA homolog, hRAD51, facilitates eukaryotic recombination/repair, although its ability to hydrolyze ATP and/or promote strand exchange appears distinct from the bacterial RecA. We have quantitatively examined the hRAD51 ATPase1 . The catalytic efficiency (kcat/K m) of the hRAD51 ATPase was approximately 50-fold lower than

stimulate DNA strand exchange (ammonium sulfate and spermidine) were found to affect the catalytic efficiency of hRAD51. The average site size of hRAD51 was determined to be ~3 nt (bp) for both ssDNA and dsDNA. Importantly, hRAD51 lacks the magnitude of ATP-induced cooperativity that is a hallmark of RecA. Together these results suggest that hRAD51 may be unable to coordinate ATP hydrolysis between neighboring protomers.

1

ATPase, ATP hydrolysis activity; bp, base pair; ssDNA, single-stranded DNA; dsDNA, doublestranded DNA; ΦX174, bacteriophage X174; ATP, adenosine triphosphate; ADP, adenosine diphosphate; AlF4-, Aluminum fluoride, DTT, dithiothreitol; EDTA, ethylenediaminetetraacetic acid; EM, electron microscopy; HEPES, N-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid]; MES, 2-(N-morpholino)ethanesulfonic acid; nt, nucleotide; RFI/III, replicative form I/III; TLC, thin-layer chromatography; TRIS, tris(hydroxymethyl)aminomethane


the RecA ATPase. Altering the ratio of DNA : hRAD51 as well as including salts which


INTRODUCTION The bacterial RecA ATPase and its homologs facilitate DNA recombination/repair, although the role of ATP hydrolysis in these processes is not fully understood (1). All members of the RecA family, including the human RAD51 protein (hRAD51), contain classic Walker A/B motifs which are fundamentally required for ATP hydrolysis (1,2). These motifs are generally conserved among proteins that bind and hydrolyze NTPs (3). RecA proteins mutated at the Walker A/B

RecA Walker A/B mutants remain viable, they display dramatically reduced levels of recombination and increased radiation sensitivity (5). Multiple mitotic and meiotic RecA homologs contribute to eukaryotic recombination/repair. Each of these homologs is likely to have distinct requirements for ATP binding and/or hydrolysis in recombination/repair. For example, four non-essential RecA homologs have been identified in Saccharomyces cerevisiae: RAD51, RAD55, RAD57, and DMC1 (6-9). Mutation of the Walker A/B motifs of RAD51 and RAD55 results in radiation sensitivity as well as meiotic recombination deficiency (9,10). Mutation of the DMC1 Walker A motif results in a dominant meiotic null mutant (11). However, similar mutations of RAD57 do not display radiation sensitivity and are only modestly deficient for meiotic recombination (9,10). The complexity of the recombination/repair system is further amplified in higher eukaryotes since eight vertebrate RecA homologs have been identified (12). In contrast to RecA or the yeast homologs, the vertebrate RAD51 gene appears to be required for cellular viability since Rad51-/mice display early embryo lethality and embryo-derived cell lines could not be established (13,14). Similarly, chicken DT40 B-cells lacking endogenous RAD51 were not viable (15). Taken together, these results are consistent with the notion that the RecA homologs of higher eukaryotes are not redundant. Interestingly, the chicken DT40 RAD51-deficient cells could be rescued by the overexpression of an hRAD51 Walker A/B mutant protein that was able to bind but not hydrolyze


motifs lack the ability to bind and/or hydrolyze ATP in vitro (4). While cells expressing these

Tombline and Fishel page 4 _____________________________________________________________________________ ATP (16). In addition, these rescued cells displayed no increase in radiation sensitivity compared to wild type cells, but were less efficient at facilitating recombination-dependent gene targeting at several loci (16). This data suggests that the contributions of hRAD51 ATP binding and hydrolysis to viability and recombination/repair may be distinct. Biochemical analysis has proven useful in elucidating the role of ATP hydrolysis in the recombination functions of the RecA protein. It has been suggested that cycles of ATP hydrolysis allow protomers within the RecA nucleoprotein filament to alternate between distinct ATP and ADP bound conformational states (1,17). The cycling between conformational states appears to drive

were suspected to facilitate strand exchange by redistributing protomers within the nucleoprotein filament. This assumption was based upon the differential affinities of RecA for DNA in the presence of ATPγS (high affinity) versus in the presence of ADP (low affinity) (1,17). An alternative model suggested that strand exchange is facilitated by ATP hydrolysis-dependent rotation of the RecA nucleoprotein filament (18). Time lapse EM of RecA nucleoprotein filaments formed in the presence of ATPγS appeared consistent with this latter proposal (19). These slowly hydrolyzing nucleoprotein filaments remained in an extended, yet dynamic state, where the protomers appeared to rotate . The coupling of ATP binding/hydrolysis to recombination by hRAD51 is less certain. In comparison to EM images of RecA, the hRAD51•ssDNA nucleoprotein filaments formed in the presence of ATPγS appeared less extended, suggesting a diminished response to ATP (20). Yet, ATP was required for hRAD51 to extend the helical pitch (DNA-unwinding) of dsDNA (20) as well as to promote strand exchange between homologous DNA substrates (21-24). Several recent studies suggest that hRAD51 can be induced to resemble RecA, both structurally and functionally. hRAD51 forms an extended nucleoprotein filament with the transition-state mimetic ADP-AlF4- that appears analogous to activated RecA (19). Two additional reports indicated that yeast and human RAD51-mediated DNA strand exchange is greatly enhanced


directional strand exchange during recombination. Historically, these alternating conformations

Tombline and Fishel page 5 _____________________________________________________________________________ by ammonium sulfate and/or spermidine (25,26). The mechanistic basis for ammonium sulfate and spermidine stimulation of RAD51 function is unknown. It is important to note that the rate of RAD51 strand exchange remains 3-5 fold lower than RecA (25,26). Furthermore, RAD51 converts a maximum of 30-60% of ssDNA to Form II products in 60 min., while RecA converts 100% ssDNA to Form II in 15 min. (25,26). Strand exchange by RecA has been shown to be largely independent of ATP hydrolysis (27-30). However, RecA-dependent bypass of heterologous DNA absolutely requires ATP hydrolysis (30-32). ATP-hydrolysis dependent bypass of heterologous DNA has been argued to

exchange reaction (30,33,34). RAD51 displays a dramatically reduced capacity to bypass heterologous DNA during strand exchange (26,35-37). Taken together, these observations suggest that altered ATP processing might account for the disparities between hRAD51 and bacterial RecA activities. To understand the ATP-dependent recombination functions of hRAD51, we have performed the first quantitative examination of the hRAD51 ATPase. Our results allow a detailed comparison with the bacterial RecA protein, the only other homolog in this family in which similar studies have been performed. Of particular importance is our observation that hRAD51 appears to lack the magnitude of ATP-induced cooperativity displayed by RecA. Our results suggest that other regulatory factors or RecA homologs may be required to assemble and control an hRAD51 nucleoprotein filament.

MATERIALS AND METHODS Materials - Chemicals of the highest grade were obtained from Amresco (Solon, OH) or Sigma (St Louis, MO). Phosphoric/Sulfuric Acid washed charcoal was obtained from Sigma (catalog# C-5510). ATP was purchased from Pharmacia, dissolved in water and adjusted for pH. ATP


require the generation of rotory torque and/or recycling of the RecA protomers during the strand

Tombline and Fishel page 6 _____________________________________________________________________________ concentration was determined by absorbance at 260nm with ε = 1.54x104. γ-[32P]-ATP was purchased from NEN Dupont.

ΦX174 DNA was purchased from New England Biolabs

(Beverly, MA). Linear, blunt ended dsDNA (RFIII) was prepared by treatment of ΦX174 dsDNA (RFI) with endonuclease StuI (New England Biolabs) followed by phenol extraction and ethanol precipitation. The DNA was resuspended in 10 mM TRIS-HCl (pH 8), 1 mM EDTA and analyzed by agarose gel electrophoresis. The concentration of DNA is expressed as moles of nt (ssDNA) or bp (dsDNA).

modifications. Briefly, hRAD51 cDNA was sub-cloned into pET24d (Novagen) and induction was performed in the E. coli strain BLR21pLysS. Cells were lysed by three freeze/thaw cycles and centrifuged at approximately 160,000 x g for one hour.

The supernatant was dialyzed

overnight against 4L of 100mM TRIS-Acetate (pH 7.5), 5% glycerol, and 7mM Spermidine HCl. The hRAD51 precipitate was collected by centrifugation and resuspended [~10 mg/mL] in P buffer (100mM potassium phosphate [pH 7.0], 10% glycerol, 150mM NaCl, 1mM EDTA, 1mM DTT) (Fraction I).

Fraction I was separated by chromatography through Reactive Blue-4

Agarose (Sigma). Protein was eluted with a 750mM step of NaCl and dialyzed overnight against 4L of H buffer (20mM HEPES [pH 7.5], 150mM NaCl, 10% glycerol, 1mM EDTA, 1mM DTT) (Fraction II). Fraction II was loaded onto a Heparin Sepharose CL-6B column, and eluted with a 750mM NaCl step (Fraction III). Fraction III was dialyzed overnight against 4L of H buffer (Fraction IV), loaded onto a Mono-Q column (HR5/5 prepacked from Pharmacia) and eluted with a gradient of 150-750mM NaCl over 20 ml (Fraction V). hRAD51 was dialyzed twice against 2L of modified H buffer (containing 0.1mM EDTA) and was stored on ice. Occasionally, an additional purification step was necessary to remove trace contaminants. In this case, the protein was dialyzed against modified P buffer (P buffer containing 100mM NaCl) after Mono-Q, chromatographed on a Mono-S column equilibrated with modified P buffer, and eluted with a 15


Purification of hRAD51 - hRAD51 was purified as previously described (38) with several

Tombline and Fishel page 7 _____________________________________________________________________________ mL gradient of 100-750mM NaCl. This was followed by dialysis against modified H buffer (0.1mM EDTA). Purified hRAD51 can be stored in modified H buffer at 0oC or -80oC for several months without appreciable loss of ATPase activity. Protein concentration was determined by amino acid analysis (Keck Facility, Yale University). Preparations were found to be nuclease free by incubation with both single and double stranded phage DNA, as well as small oligonucleotides.

ATP hydrolysis - Unless otherwise indicated the 10µL reactions contained 1µM hRAD51 and

150mM NaCl, 10% glycerol, 1mM DTT, 2mM MgAcetate). In addition to the indicated amounts of ATP, 1µCi of γ-[32P]-ATP was included in each reaction. To achieve consistency in such small reactions, mixes containing either DNA/ATP or hRAD51 were added separately using a repeat pipettor (Eppendorf). Reactions were initiated by adding the hRAD51 mix last and incubated at 37oC for 30-60 min. in an Ericomp thermal cycler with a heated lid to prevent evaporation. 400µL of ice cold 10% activated charcoal (Norit) in 10mM EDTA was added to terminate the reactions. Tubes were vortexed and placed on ice for a minimum of 3 hours to allow maximal binding of free ATP to the charcoal. After centrifugation for 30 min., two 50µL aliquots were counted by the Cherenkov method. hRAD51 was omitted from two additional reactions which contained either the lowest or highest amount of ATP. After processing with Norit, background hydrolysis determined for these reactions was averaged and subtracted from reactions containing hRAD51. In general, there was no significant difference in background between lowest and highest ATP reactions. Total counts in each reaction were determined by the Cherenkov method for duplicate reactions that had not been processed with Norit. The average of at least three such duplicates was taken for the total cpm/reaction. Specific activity of ATP in (cpm/mol; γ-[32P]-ATP : ATP) in each was calculated by dividing the total counts in each reaction by the amount of total ATP. The amount of ATP hydrolyzed (mol) in each reaction was determined by dividing the adjusted


6µM DNA (nt or bp). All reactions were performed in a standard buffer (20mM HEPES pH 7.5,

Tombline and Fishel page 8 _____________________________________________________________________________ hydrolysis value (cpm) by the specific activity of ATP in each reaction. Molar ratios were varied by adjustment of the DNA or hRAD51 concentrations in otherwise identical reactions. In all reactions, conditions were normalized for the DNA or hRAD51 storage buffers. The pH was varied using similar reaction buffers except that MES was used for the range between pH 6.2 and pH 7.2 and HEPES was varied between pH 7.2 and pH 8.2. For ATPase reactions containing additional salts, 0.5µL of 2M (NH4)2SO4 (pH 8.0) and/or 0.5µL of 80mM spermidine HCl were added to reactions with a final volume of 10µL yielding final concentrations of 100mM and/or 4mM respectively. These reactions processed as above.

ATP dependence of hydrolysis - Using a modification of a previously published method (38), we purified hRAD51 to near homogeneity (Fig. 1). The ATPase activity of hRAD51 was measured by the Norit method (see Materials and Methods) and the unique conversion of ATP to ADP was confirmed by thin-layer chromatography (TLC)(39). We found the Norit method to be superior to TLC or polyacrylamide gel electrophoretic (PAGE) analysis because of the ease of data acquisition, reduced expense, and the large number of analyses that could be performed in tandem. Past experience has suggested that the separation efficiency of Norit exceeds 90% and can be increased by prolonged incubation of the terminated reactions at 0˚C (39,40). While a previous report indicated that ATP hydrolysis by hRAD51 was very inefficient (kcat•ssDNA = 0.2min-1, kcat•dsDNA = 0.1min-1, kcat = 0.03min-1), these values were based on a single ATP concentration (200µM) (21). To confirm and extend these studies, as well as examine the rate limiting step(s) within the hydrolysis cycle, we performed classic Michealis-Menten analysis to define the Km and kcat (Vmax/[hRAD51]o). We determined these values for the hRAD51 ATPase activity in the presence of ssDNA, supercoiled dsDNA (RFI), linear dsDNA (RFIII), and in the absence of DNA. The kcat values (kcat•ssDNA = 0.21 min-1; kcat•dsRFI = 0.1 min-1; kcat•dsRFIII = 0.07 min-


RESULTS

Tombline and Fishel page 9 _____________________________________________________________________________ 1 ; kcat = 0.07 min-1; Fig. 2A, 2B, and Table I) agreed with values previously reported (21). These data indicate that the kcat•ssDNA for hRAD51 is approximately 150-fold lower than bacterial RecA (kcat•ssDNA = 28 min-1) and the kcat•dsDNA is approximately 220-fold lower than bacterial RecA (kcat•dsDNA = 22 min-1 at pH 6.2) (41-43). The kcat in the absence of DNA is approximately 4-fold higher than the bacterial RecA (kcat = 0.015min-1)(41-43). In addition, hRAD51 displays an equal or higher apparent affinity for ATP (Km•ssDNA = 23+3µM; Km•dsDNA(RFI) = 27+4µM; Km•dsDNA(RFIII) = 26+5µM; Km = 110+22µM) compared to bacterial RecA (S0.5•ssDNA ≈ 20-60µM; S0.5•dsDNA(RFI) ≈ 100µM at pH 6.2; S0.5 ≈ 100µM; (17,41); the substrate concentration where half-maximal activity In

general, DNA appears to decrease the hRAD51 Km equivalently (Fig. 2A, 2B, and Table I). Calculation of the hRAD51 ATPase catalytic efficiency (kcat/Km) suggests that ssDNA (150 sec1

M-1) induces the ATPase no more than 2-3 fold greater than dsDNA (≈ 68 sec-1M-1) and at least

5-fold greater than in the absence of DNA (11 sec-1M-1). The catalytic efficiency of hRAD51 is approximately 50-fold less than bacterial RecA (8300 sec-1M-1).

hRAD51 lacks ATP-induced cooperativity – A commonly used method for determining ATPinduced cooperativity is by calculating the Hill Coefficient (44).

The Hill Coefficient was

originally developed for the analysis of cooperative fractional saturation for a ligand binding to multiple interdependent sites (45). If one assumes that the rate of an enzymatic reaction is proportional to the fractional saturation of the enzyme, then a slope (Hill Coefficient) greater than one derived from a plot of the fractional rate [v/(Vmax-v)] versus the substrate concentration ([S]) indicates positive cooperativity (44). In general, the largest value for cooperativity occurs at halfmaximal fractional saturation. As the fractional saturation approaches unity, the Hill Coefficient also approaches 1. This appears to be the case for the RecA ATPase (41,46).

The Hill

Coefficient (nH) of RecA varies from nH = 3 to nH = 11 at ATP concentrations below or slightly


occurs is S 0.5 in a cooperative system and equals Km in a non-cooperative system; (44).

Tombline and Fishel page 10 _____________________________________________________________________________ above the S 0.5. At ATP concentrations above the S 0.5 (>100µM), ATP-induced cooperativity becomes less apparent since the Hill Coefficient equals 1. Three methods of analysis of hRAD51 ATPase data indicate that hRAD51 lacks ATPinduced cooperativity. First, in the absence or presence of DNA, the rate of ATP hydrolysis was easily fit to a simple hyperbolic curve (the Michaelis–Menten equation; Fig. 2A). Second, the slope of the same ATPase data plotted by the double-reciprocal method is linear (not concave upward; Fig. 2B). Third, the slope of hRAD51 ATPase data plotted as a fractional rate versus ATP concentration (Hill Coefficient) was approximately 1 in all conditions (ssDNA nH = 0.79;

Table I). hRAD51 also failed to display ATP-induced cooperativity in the range of ATP concentrations below the Km (Fig. 3) These data contrast the cooperativity shown by RecA.

The effect of pH on the hRAD51 ATPase - RecA can efficiently utilize dsDNA as a cofactor for hydrolysis at pH 6.2. However, at pH 8.0 the dsDNA-dependent ATPase can only be measured after a several hour lag (1,17,42). This lag at higher pH is absent when the carboxyl-terminal domain of bacterial RecA is deleted or when purified unwound dsDNA (form X) was used as a cofactor (43,47,48). We examined the pH dependence of the hRAD51 ATPase between 6.2 and 8.2 and found no difference in ATPase activity for either ssDNA or dsDNA (RFIII) (Fig. 4A and 4B, respectively). It is interesting to note that a comparison of the hRAD51 and RecA sequences suggests that the carboxyl-terminal domain is missing in hRAD51 (1,2,49).

High Salt Activation of the hRAD51 ATPase – In the absence of DNA, high salt concentrations increased the kcat of bacterial RecA ATPase to a value that is equivalent to the kcat•ssDNA observed at low salt concentrations. However, the high salt-dependent RecA ATPase reaction displays a Km that approaches 1 mM and fails to display ATP-induced cooperativity (50).

ATPase activity

under these conditions has been generally attributed to salt-induced structural transitions within


dsDNA (RFI) nH = 0.76; dsDNA (RFIII) nH = 0.74; absence of DNA nH = 0.70; Fig. 2C and

Tombline and Fishel page 11 _____________________________________________________________________________ the RecA nucleoprotein filament (51). High salt (1.5M NaCl) also increases the hRAD51 ATPase activity (kcat = 0.40 min-1; Fig. 5A and Table I) such that it approaches the ATPase activity observed with low salt in the presence of ssDNA (150mM NaCl; kcat•ssDNA = 0.21 min-1; Fig. 2A and Table I). In addition, hRAD51 fails to display ATP-induced cooperativity in high salt (nH = 0.8; Fig. 5B and Table I). In contrast to RecA, the Km of the hRAD51 ATPase in high salt (Km = 17 µM) resembles the Km at low salt when DNA is present (Km ≈ 20 µM).

While the Km

represents a number of variables (44), these results are consistent with the notion that hRAD51 is incapable of forming an actively hydrolyzing aggregate (see ref. (50).

suggested that DNA concentration affects both the Km and Vmax (Figs. 6A, 6B and Table II). The RecA protein displays a reduction in S0.5 at elevated DNA concentrations similar to that observed with hRAD51 (52). However, the Vmax of RecA appeared unaffected by elevated DNA concentration while the Vmax of hRAD51 displayed a peak between 3-9 nt ssDNA per hRAD51 monomer and then decreased at high ssDNA concentrations (52). Calculation of the catalytic efficiency (kcat/Km) with ssDNA appears to indicate an optimum ratio of 6-8 nt ssDNA: 1 hRAD51 monomer. In contrast, the catalytic efficiency of the hRAD51 ATPase in the presence of dsDNA did not display an optimum. The Hill coefficient appeared to remain constant nH ≈1 at all ratios of DNA : hRAD51 (data not shown). This observation contrasts similar studies with RecA where a 20 nt:1 RecA ratio resulted in a Hill coefficient greater than nH = 11 (46).

The site size of the hRAD51 ATPase – The hRAD51 ATPase appeared to increase linearly with increasing hRAD51 protein (Fig. 7A). This linear increase was evident in the absence of DNA as well as in the presence of ssDNA and dsDNA. A clear saturation of the hRAD51 ATPase (v) was observed at a molar ratio of 3-4 nt : 1 hRAD51 (Fig. 7B; see also Fig. 6A). Interestingly, there appeared to be an initial saturation of ATPase activity that occurred at approximately a 1 nt :


DNA dependence of the hRAD51 ATPase - Michaelis-Menten analysis of the hRAD51 ATPase

Tombline and Fishel page 12 _____________________________________________________________________________ 1 hRAD51 monomer molar ratio (Fig. 7B). These data suggest that the hRAD51 ATPase may possess two modes of DNA stimulation. The bacterial RecA site size (N) appeared to vary between 3 and 6 nucleotides per monomer and was dependent upon whether ATP hydrolysis or DNA binding was measured (17). This paradox was resolved by dividing the vATPase/[DNA] (at constant excess protein) by the vATPase/[protein] (at constant excess DNA) and revealed that N ≈ 3(53). Using this methodology, we examined the site size of hRAD51 for both ssDNA and dsDNA (Table III and Table IV). We found that the vATPase/[DNA] for RecA remained constant with increased DNA concentrations,

range of site-sizes that depended upon calculations using the average vATPase/[protein] and individual vATPase/[DNA] values (Table III) or the average vATPase/[DNA] and individual vATPase/[protein] values (Table IV). While averages of these calculations yielded a site size of approximately 3 nt (bp), these values appeared to be too variable to provide a precise determination.

The effect of ammonim sulfate and spermidine on the hRad51 ATPase – Two recent reports demonstrate that extensive DNA strand exchange promoted by the yeast and human RAD51 proteins could be induced with ammonium sulfate and/or spermidine (25,26). Under these modified conditions hRAD51 displays a reduced affinity for dsDNA (25) and the transition from intermediates to products during DNA strand exchange was enhanced (26). Although ATPase activity was not examined, these studies suggested that ammonium sulfate and/or spermidine provided a condition for efficient DNA strand exchange in the absence of significant ATP hydrolysis. To address the effects of ammonium sulfate and/or spermidine, we performed a detailed analysis of the hRAD51 ATPase under similar conditions. We found that ammonium sulfate increased the Km approximately 3-4 fold in the presence of ssDNA (Fig. 8A) or dsDNA (Fig. 8B) cofactors (Table V). In contrast, spermidine did not significantly affect the hRAD51


while the vATPase/[DNA] of hRAD51 decreased significantly (Table III). These results produced a

Tombline and Fishel page 13 _____________________________________________________________________________ ATPase (Fig. 8; Table V). Ammonium sulfate also elicited a modest decrease in the rate of hydrolysis (Vmax) in the presence of dsDNA (Fig. 8B; Table V). However, the rate of hydrolysis was modestly enhanced in the presence of ssDNA (Fig. 8A; Table V). It is worth noting that under both conditions (ammonium sulfate and/or spermidine) the Hill coefficient remained approximately 1 (data not shown) and the data was easily fit to the Michaelis-Menten equation (Fig. 8).

ATP binding and hydrolysis are coupled to the recombinational strand exchange function(s) of bacterial RecA (1,4,17). This is exemplified by the observation that the free-energy of strand exchange and ATP hydrolysis appear equivalent in temperature-dependent studies (54). In addition, coordinated ATP hydrolysis appears exceedingly efficient between protomers within the RecA nucleoprotein filament (Hill coefficient > 11). The ATP hydrolysis activity of other RecA family members has not been well characterized. Initial studies suggested that hRAD51 was inefficient at promoting extensive recombinational strand exchange and displayed a weak ATPase activity compared to RecA (21-23). More recent studies have demonstrated enhanced RAD51 strand exchange activity in the presence of ammonium sulfate and spermidine (25,26). Our studies were initiated to detail the mechanistic differences between RecA and hRAD51. The hRAD51 ATPase appears fundamentally distinct from RecA. As has been previously reported (21,22), the kcat for hRAD51 is approximately 150 to 200-fold lower than the kcat for the bacterial RecA.

Combined with the 2-3 fold lower Km of hRAD51 reported here, these

observations translate to an approximately 50-fold difference in the catalytic efficiency (kcat/Km) of hRAD51 compared to the bacterial RecA. The catalytic efficiency of hRAD51 is approximately 7 orders-of-magnitude below a diffusion-limiting process (55).


DISCUSSION

Tombline and Fishel page 14 _____________________________________________________________________________ The majority of sequence homology between hRAD51 and RecA is within a central domain containing classic Walker A/B adenosine nucleotide binding motifs (1,2,49). hRAD51 contains an N-terminal domain which is absent in RecA and is missing a C-terminal domain that is present in RecA (1,2,49). Based upon NMR and mutagenesis data, it has been suggested that the N-terminus of hRAD51 may functionally substitute for the C-terminus of RecA (56). However, the hRAD51 ATPase activity reported here appears to largely resemble the ATPase activity of a C-terminal truncated mutant of RecA (RecA5327). The kcat of the RecA5327 mutant was stimulated by both ssDNA and dsDNA equally and without a lag (48). Likewise, the kcat of

acidic pH allowed the RecA to utilize dsDNA as a co-factor for ATP hydrolysis without a lag, an effect that has been generally ascribed to charge neutralization of the C terminal domain (1). However, a range of pH had no effect on the hRAD51 ATPase. These data suggest that the hRAD51 N-terminus may not fully substitute for the RecA C-terminus. We determined the DNA site size of the hRAD51 ATPase to be approximately 3 nt (bp) for ssDNA or dsDNA.

Similar methodologies were used to determine that the bacterial RecA

has a site size of 3 nt for ssDNA (53). This correlative site size (3 nt or bp) for hRAD51 appears to indicate that most of the protein in the purified fractions was active. While we have estimated the minimal site size of hRAD51 to be 3 nt, 6-8 nt ssDNA per hRAD51 monomer provoked the optimal catalytic efficiency of the hRAD51 ATPase. This observation may indicate that hRAD51 binds an additional ssDNA molecule, similar to RecA. Saturation of a second RecA ssDNA binding site reduced the S 0.5 from 60µM to approximately 20µM. However, the Vmax and ATPinduced cooperativity of RecA remained unaffected by excess ssDNA (52,53). In contrast, excess ssDNA lowered the Vmax of the hRAD51 ATPase and the Km approached the KD for ATP binding (57). While the effect of excess ssDNA on the S 0.5 of RecA appeared similar to hRAD51, the RecA ATPase retained ≈ 10-fold difference between the S 0.5 and KD for ATP binding. The persistent difference between the S 0.5 and KD of RecA is thought to correlate with a threshold of


hRAD51 in the presence of ssDNA or dsDNA appeared only modestly different. Moreover,

Tombline and Fishel page 15 _____________________________________________________________________________ nucleoprotein filament ATP saturation which must precede efficient/cooperative ATP hydrolysis (17). It may be that the hRAD51 ATPase is not subject to regulation by a threshold of ATP saturation. The reduced Vmax displayed by the hRAD51 ATPase in the presence of excess ssDNA also suggests a change in rate limiting step (see (57). It is notable that the hRAD51 ATPase fails to display the magnitude of ATP-induced cooperativity found with the RecA ATPase. Whether the lack of ATP-induced cooperativity is responsible for the reduced catalytic efficiency of the hRAD51 ATPase and/or the distinct recombinational strand exchange is uncertain. It is suspected that ATP-induced cooperativity

achieving the active/extended nucleoprotein filament by saturation of a threshold number of RecA protomers with ATP (1,17,58), and 2.) maintaining the active/extended nucleoprotein filament during ATP hydrolysis by provoking rapid ADP release (thereby preventing reversibility) (59,60). In the case of RecA, the cooperative state of the nucleoprotein filament appears critical for recombinational strand exchange as well as bypass of heterologous DNA during strand exchange (1,17) (30-32). Specialized cellular or biochemical conditions may induce hRAD51 to achieve and/or maintain an active nucleoprotein filament that is necessary for efficient recombination functions. Such conditions could enhance the rate and cooperativity of the hRAD51 ATPase. Alternatively, such conditions may allow hRAD51 to more effectively utilize ATP but not dramatically affect ATP hydrolysis. In the presence of ammonium sulfate we observed a modest decrease in the rate of hRAD51-mediated ATP hydrolysis when dsDNA was used as the cofactor. This data appears consistent with the interpretation of Sigurdsson et al. which suggested that ammonium sulfate enhanced the ability of hRAD51 to discriminate between ssDNA and dsDNA (25). The most significant effect of ammonium sulfate is to increase the Km for ATP 3- to 4-fold. The molecular effect of ammonium sulfate on the hRAD51 protein is unknown. However, recent studies with the F1 ATPase suggest that SO4- is capable of occupying an intermediate position near the region


augments the catalytic efficiency of the RecA ATPase at two potential rate-limiting junctures: 1.)

Tombline and Fishel page 16 _____________________________________________________________________________ of the γ-phosphate that, with ADP, mimics an ATP hydrolysis intermediate (61). We have found that ADP release appears rate-limiting for the hRAD51 ATPase (57). Perhaps ammonium sulfate provokes transient ternary hRAD51•ADP•SO4- complexes that maintain and mimic a more active ATP-bound nucleoprotein filament. Such complexes would be distinct from fully ADP-bound inactive nucleoprotein filaments and may promote efficient DNA strand exchange without dramatically enhancing the rate of hydrolysis. It is important to note that even in the presence of ammonium sulfate and spermidine RAD51 does not appear to be capable of bypassing heterologous DNA during strand exchange (25,26). Our studies appear to suggest that it is the

bypassing heterologous DNA during strand exchange largely refractory. The present studies are consistent with at least two possibilities. One possibility is that the role of ATP binding and hydrolysis by hRAD51 in recombination/repair is different than RecA. Alternatively, other factors may be required to mimic the enhancing effect(s) of ammonium sulfate and/or improve the efficiency of hRAD51.

ACKNOWLEDGMENTS The authors thank Hans-Jürg Alder and the Kimmel Nucleic Acids Facility for oligonucleotide synthesis and sequencing, Pete Von Hippel, Charles Brenner, Jan Hoek , Albert Wong, Christoph Schmutte, Kang-Sup Shim, Chris Heinen, Samir Acharya, Scott Gradia, and Teresa Wilson for helpful discussions and Kristine Yoder for helping revise the manuscript. This work was supported by NRSA training grant 5-T32-CA09678 (GT) and NIH grant CA56542 (RF).


continued inability of RAD51 to coordinate ATP hydrolysis between protomers that makes


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Biology 290, 495-504

Table I Summary of hRAD51 ATPase data (see Fig. 2 and 5) Condition

Km (µM)

Vmax (µM•min-1)

kcat (min-1)

kcat / Km (s-1 •M-1)

Hill coeff. (nH)

ssDΝΑ dsDΝΑ (RFI) dsDΝΑ (RFIII) No DNA 1.5M NaCl

23 + 3 27 + 4 26 + 5 110 + 22 16.9 + 2

0.211 + 0.005 0.114 + 0.003 0.071 + 0.002 0.073 + 0.006 0.197 + 0.006

0.21 0.11 0.07 0.07 0.20

150 68 45 11 190

0.79 0.76 0.74 0.70 0.81

nt ssDNA

Km

Vmax

(µM)

(µM) 11.4+4.8 35+5.0 23+9.9 13.2+7.4 10.9+3.0 8.1+4.9 3.6+5.0

(µM•min-1)

0.5 1.0 1.5 3.0 4.5 6.0 15.0 bp dsDNA(RFI) (µM)

0.5 1.0 1.5 3.0 4.5 6.0 15.0

Km (µM) 8.5+4.7 13+11.5 9.7+6.2 20.3+6.6 8.8+5.6 21.4+7.0 6.34+5.0

0.073+0.006 0.122+0.006 0.148+0.018 0.164+0.018 0.165+0.008 0.129+0.012 0.087+0.012

Vmax (µM•min-1) 0.072+0.001 0.083+0.015 0.113+0.013 0.126+0.010 0.064+0.009 0.130+0.012 0.079+0.005


Table II DNA dependence of the Km and Vmax for hRAD51-mediated ATP hydrolysis. Km and Vmax were determined by Michaelis-Menten analysis (see also Fig. 6).

Table III ATPase data as a function of DNA concentration to determine site size (N). v was determined by incubating the indicated amount of DNA with 3µM hRAD51. Each 10µL reaction contained 250µM ATP and was incubated at 37°C for 45 min. Site size (N) was determined by dividing v / [DNA] by average kcat values obtained from experiments where [hRAD51] was varied in the presence of excess DNA (Table IV). An average of the ssDNA site sizes (when hRAD51 was in excess) indicated that N ≈ 2.85 + 0.76 nt. Excluding the 0.5µM hRAD51 concentration (N = 9.14), the same analysis for dsDNA indicated that N ≈ 3.08 + 1.11 bp. nt ssDNA µM) (µ

µM) (µ

0.16 0.33 0.50 0.66 0.83 1.66 3.33 5.0 6.66 8.33 DNA : RAD51 (bp : monomer)

0.5 1 1.5 2 2.5 5 10 15 20 25

0.16 0.33 0.50 0.66 0.83 1.66 3.33 5.0 6.66 8.33

bp dsDNA(RFI)

v

v / [DNA]

µM•min-1) (µ 0.32 + 0.03 0.58 + 0.08 0.73 + 0.06 0.79 + 0.10 0.79 + 0.06 0.89 + 0.02 1.35 + 0.07 1.49 + 0.07 1.53 + 0.07 1.54 + 0.20

(min-1) 0.64 + 0.055 0.58 + 0.077 0.49 + 0.041 0.40 + 0.048 0.32 + 0.022 0.18 + 0.005 0.14 + 0.007 0.10 + 0.005 0.08 + 0.003 0.06 + 0.008 v / [DNA] (min-1) 1.06 + 0.112 0.53 + 0.011 0.38 + 0.025 0.28 + 0.051 0.24 + 0.044 0.14 + 0.010 0.09 + 0.010 0.08 + 0.008 0.06 + 0.002 0.05 + 0.005

v µM•min-1) (µ 0.53 + 0.05 0.53 + 0.01 0.57 + 0.04 0.55 + 0.10 0.61 + 0.10 0.70 + 0.05 0.92 + 0.10 1.24 + 0.13 1.30 + 0.05 1.26 + 0.12

Site size (N) 3.76 3.40 2.88 2.35 1.88

NA NA NA NA NA

Site size (N) 9.14 4.57 3.28 2.41 2.07 NA NA NA NA NA


0.5 1 1.5 2 2.5 5 10 15 20 25

DNA : RAD51 (nt : monomer)

Table IV ATPase data as a function of hRAD51 concentration to determine site size (N). v was determined by incubating the indicated amount of hRAD51 with 6µM DNA. Each 10µL reaction contained 250µM ATP and was incubated at 37°C for 30 min. kcat values were averaged for reactions performed in the presence of either ssDNA (average kcat = 0.170) or dsDNA (average kcat = 0.116). These average kcat values were used to determine site sizes by comparison with experiments when DNA was varied (Table III). The site size (N) was determined by dividing the average v/[DNA] value obtained for ssDNA (0.486) or dsDNA (0.358) by each individual v/ [hRAD51] obtained at various hRAD51 concentrations. Using this approach, the site size (N) = 2.66 + 0.62 nt ssDNA or N = 2.81 + 0.89 bp dsDNA (see also Fig. 7). ssDNA:R51

v

kcat

(µM)

(nt : monomer)

(µM•min-1)

0.1 0.3 0.6 1.0 2.0 3.0

60 : 1 20 : 1 10 : 1 6:1 3:1 2:1

0.022 + 0.010 0.065 + 0.013 0.104 + 0.024 0.172 + 0.032 0.272 + 0.035 0.449 + 0.057

(v / [hRAD51]) (min-1) 0.218 + 0.103 0.218 + 0.043 0.173 + 0.041 0.172 + 0.032 0.136 + 0.017 0.150 + 0.019

hRAD51

dsDNA:R51

v

kcat

(µM)

(bp : monomer)

(µM•min-1)

0.1 0.3 0.6 1.0 2.0 3.0

60 : 1 20 : 1 10 : 1 6:1 3:1 2:1

0.034 + 0.007 0.046 + 0.003 0.062 + 0.014 0.118 + 0.009 0.212 + 0.019 0.288 + 0.034

(v / [hRAD51]) (min-1) 0.259 + 0.067 0.156 + 0.009 0.114 + 0.023 0.109 + 0.009 0.097 + 0.010 0.095 + 0.011

Site size (N) 2.23 2.23 2.81 2.81 3.57 3.24

Site size (N) 1.38 2.29 3.14 3.28 3.69 3.76


hRAD51

Table V Summary of the effect of Ammonium Sulfate and Spermidine on the hRAD51 ATPase

dsDNA (RFI) No Addition + (NH4)2SO4 + Spermidine + (NH4)2SO4 & Spermidine

Vmax (µM•min-1•10-2)

kcat (min1)

kcat/Km (sec-1•M-1)

9.5 + 1.6

5.5 + 0.2

0.11

193

39.8 + 4.4

7.3 + 0.3

0.15

63

12.5 + 2.9

5.4 + 0.3

0.11

146

37.5 + 5.2

6.1 + 0.3

0.12

53

Km (µM)

Vmax (µM•min-1•10-2)

kcat (min1)

kcat/Km (sec-1•M-1)

13.3 + 2.5

7.7 + 0.4

0.15

194

29.0 + 7.0

5.4 + 0.5

0.11

62

11.8 + 2.3

6.3 + 0.3

0.13

178

43.6 + 6.2

6.6 + 0.3

0.13

51


ssDNA No Addition + (NH4)2SO4 + Spermidine + (NH4)2SO4 & Spermidine

Km (µM)

102kDa 78kDa

34.2kDa

*

25kDa

Figure 1. hRAD51 purified to near homogeneity. hRAD51 (0.5 µg) was resolved by 10% SDS PAGE and subsequently silver stained. Densitometric analysis performed with a Biorad Gel Doc System revealed better than 95% purity. The major contaminant, marked by an asterisk, is approximately 30kDa and is recognized by rabbit polyclonal α-hRAD51 antibody.


49.5kDa

0.25

A v (µM•min-1)

0.20

0.15

0.10

0.05

0 0

0.1

0.2

0.3

0.4

0.5

0.6

ATP (mM) 100

B

60 40 20 0 -0.05

0

0.05

0.1

0.15

1 / ATP (mM)

log [v/(Vmax-v)]

C

1.5 1 0.5 0 -0.5 -1 0.5

1

1.5

2

2.5

3

log ATP (mM)

Figure 2. hRAD51-mediated ATP hydrolysis as a function of ATP. ATPase assays were performed by incubating 1.0 µM hRAD51, and if present, 6µM DNA (nt or bp), with the indicated amount of ATP (which was supplemented with γ-[32P]-ATP). Each reaction was incubated at 37˚C for one hour and then terminated by the addition of 10% activated charcoal (Norit) in 10mM EDTA. The samples were centrifuged and the supernatant containing free phosphate was counted by the Cherenkov method. Data points represent the average of at least three replicate experiments. A) hRAD51 ATPase data was fit to the Michaelis-Menten equation for reactions performed with (l) ssDNA (Km= 23+3; Vmax≈ 0.21), (n) dsDNA (RFI) (Km= 27+4; Vmax≈ 0.11), (o) dsDNA (RFIII) (Km= 26+5; Vmax≈ 0.07), as well as (m) in the absence of DNA (Km= 110+22; Vmax≈ 0.07). Note: all Km are expressed in µM and Vmax= µM ATP hydrolyzed•min-1 B) Double-Reciprocal Plot of the same data, and C) Hill plot of the same data (nH ≈ 1 for all cases).


1/v

80

v (µM•min-1 x 10-3)

A

3.5 3.0 2.5 2.0 1.5 1.0 0.5 0 0

1

2

3

4

5

log [v/(Vmax-v)]

B

0 -0.5 -1 -1.5 -2 -2.5 -1.5

-1

-0.5

0

0.5

1

1.5

log ATP (µM)

Figure 3. The hRAD51 ATPase does not display ATP-induced cooperativity at ATP concentrations below the Km. Each reaction contained 0.4µM hRAD51, 1.7µM ssDNA (nt) or dsDNA (RFI) (bp), and the indicated amount of ATP. Each reaction was incubated at 37˚C for 30 min. and processed with Norit as in Figure 2. Data points represent the average of at least three replicate experiments. A) ATPase data for either ssDNA (l) or dsDNA (RFI) (n) was fit to the Michaelis-Menten equation, B) In the presence of ssDNA (l) the Hill coefficient (nH) = 0.91 and in the presence of dsDNA (RFI) (n) the Hill coefficient (nH) = 0.74.


ATP (µM)

0.40

A v (µM·min-1)

0.35 0.30 0.25 0.20 0.15 0.10 0.05 0

6.2 6.4 6.6 6.8 7.0 7.2 7.2 7.4 7.5 7.6 7.8 8.0

HEPES

pH

B

0.14

v (µM•min-1)

0.12 0.10 0.08 0.06 0.04 0.02 0

6.2 6.4 6.6 6.8 7.0 7.2 7.2 7.4 7.5 7.6 7.8 8.0

MES

8.2

HEPES

pH

Figure 4. The hRAD51 DNA-dependent ATPase is not affected by pH. Each reaction contained 1.0µM hRAD51, 200µM ATP (supplemented with γ[32P]-ATP) and 6µM of either (A) ssDNA (nt) or (B) dsDNA (bp; RFIII). Each reaction was incubated for one hour at 37˚C and was processed by the Norit method as described in Figure 2. The pH was varied by using buffers made with either MES pH 6.2 - 7.2 (left side) or HEPES pH 7.2 - 8.2 (right side). Each bar represents the average of at least three separate experiments.


MES

8.2

0.25

v (µM•min-1)

A

0.20

0.15

0.10

0.05 0

0.1

0.2

0.3

0.5

-0.5

0

ATP (mM)

0.8

log [v/(Vmax-v)]

B

1

0.6 0.4 0.2 0 -0.2 -0.4 -2.5

-2

-1.5

-1

log ATP (mM)

Figure 5. hRAD51 promoted ATP hydrolysis in the presence of high salt. hRAD51 (1.0µM) was incubated with the indicated amount of ATP (mM) for one hour at 37˚C in reactions which contained 1.5M NaCl. This high salt condition stimulates hRAD51 ATPase activity to the same extent as ssDNA (both Km and kcat (Vmax/[E])). A) ATPase data was fit to the Michaelis-Menten equation. (Km = 16.9+ 2 µM, Vmax = 0.2 µM•min-1) B) A Hill plot of the same data indicates that the high salt-dependent ATPase of hRAD51 also lacks ATP-induced cooperativity (nH = 0.81).


0.4

ssDNA (nt) : hRad51 (monomer)

A

0

2

4

6

8

10

12

14

40

16 0.20

0.15

30 0.10 20 0.05

10

0 0

2

4

6

8

10

12

0 16

14

16

nt (µM) dsDNA (bp) : hRad51 (monomer)

B

0

2

4

6

8

10

12

40

0.20

0.15

30 0.10 20 0.05

10

0 0

2

4

6

8

10

12

14

Vmax (µM•min-1) (m)

Km (µM) (l)

50

0 16

bp (µM) Figure 6. The molar ratio of DNA : hRAD51 affects both Vmax and Km of the hRAD51 ATPase. For each ratio of hRAD51: DNA both Km (l) and Vmax (m) represent average values for a set of 8 different ATP concentrations performed in triplicate. These values were obtained by fitting the initial rate of hydrolysis to the Michaelis-Menten equation . Each reaction within a set contained 1.0µM hRAD51, the indicated amount of (A) nt ssDNA or (B) bp dsDNA (RFI), and a variable amount of ATP (supplemented with γ-[32P]-ATP). Each was incubated at 37˚C for one hour and subsequently processed with Norit as in Figure 2. This data is summarized in Table II.


14

Vmax (µM•min-1) (m)

Km (µM) (l)

50

A

0.5

v (µM•min-1)

0.4 0.3 0.2 0.1 0 0

0.5

1

1.5

2

2.5

3

3.5

B v (µM•min-1)

1.6 1.2 0.8 0.4 0 0

5

10

15

20

25

nt or bp DNA (µM)

Figure 7. hRAD51 and DNA dependence of ATP hydolysis. ATPase reactions were varied by mixing (A) the indicated amount of hRAD51with 6µM DNA (nt or bp) or (B) the indicated amount of DNA with 3µM hRAD51. Each reaction contained 250µM ATP and was incubated for 30 min. at 37˚C. Each reaction was processed by the Norit method as in Figure 2. Each point represents the average of three replicate experiments. (l) indicates reactions where ssDNA was added; (n) indicates reactions where dsDNA (RFI) was added; and (m) indicates reactions performed in the absence of DNA.


hRad51 (µM)

A

8

v (µM•min-1•10-2)

7 6 5 4 4.0 3.5

3

3.0 2.5

2

2.0 1.5 1.0

1 0

0.5 0 0

0

50

100

5

10

150

15

20

25

200

30

250 Downloaded from http://www.jbc.org/ by guest on October 12, 2017

ATP (µM) 8

B v (µM•min-1•10-2)

7 6 5 4 4.0

3

3.5 3.0 2.5

2

2.0 1.5

1 0 0

1.0 0.5 0 0

50

100

150

5

10

15

200

20

25

30

250

ATP (µM) Figure 8. The effect of ammonium sulfate and spermidine on the hRAD51 ATPase. ATPase assays were performed by incubating 0.5µM hRAD51, and if present, 6µM (A) ssDNA (nt) or (B) dsDNA (bp), with the indicated amount of ATP (which was supplemented with γ-[32P]-ATP). Each reaction was incubated at 37˚C for one hour and then terminated by the addition of 10% activated charcoal (Norit) in 10mM EDTA. The samples were centrifuged and the supernatant containing free phosphate was counted by the Cherenkov method. Data points represent the average of at least three replicate experiments. ATPase data was fit to the Michaelis-Menten equation. ATPase reactions were performed under standard buffer conditions (l), in the presence of 100mM (NH4)2SO4 (u), in the presence of 4mM spermidine (s), or in the presence of 100mM (NH4)2SO4 and 4mM spermidine (n). Insets clearly indicate the effect of (NH4)2SO4 on Km values. This data is summarized in Table V.

Biochemical characterization of the human RAD51 Protein: I. ATP hydrolysis Gregory Tombline and Richard Fishel J. Biol. Chem. published online February 11, 2002

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