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Bilyard T, Nakanishi-Matsui M, Steel BC, Pilizota T, Nord AL, Hosokawa H, Futai M, Berry RM. High-resolution single-molecule characterization of the enzymatic states in Escherichia coli F1-ATPase. Philos Trans R Soc Lond B Biol Sci 2012; 368:20120023. [PMID: 23267177 DOI: 10.1098/rstb.2012.0023] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rotary motor F(1)-ATPase from the thermophilic Bacillus PS3 (TF(1)) is one of the best-studied of all molecular machines. F(1)-ATPase is the part of the enzyme F(1)F(O)-ATP synthase that is responsible for generating most of the ATP in living cells. Single-molecule experiments have provided a detailed understanding of how ATP hydrolysis and synthesis are coupled to internal rotation within the motor. In this work, we present evidence that mesophilic F(1)-ATPase from Escherichia coli (EF(1)) is governed by the same mechanism as TF(1) under laboratory conditions. Using optical microscopy to measure rotation of a variety of marker particles attached to the γ-subunit of single surface-bound EF(1) molecules, we characterized the ATP-binding, catalytic and inhibited states of EF(1). We also show that the ATP-binding and catalytic states are separated by 35±3°. At room temperature, chemical processes occur faster in EF(1) than in TF(1), and we present a methodology to compensate for artefacts that occur when the enzymatic rates are comparable to the experimental temporal resolution. Furthermore, we show that the molecule-to-molecule variation observed at high ATP concentration in our single-molecule assays can be accounted for by variation in the orientation of the rotating markers.
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Affiliation(s)
- Thomas Bilyard
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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2
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Li B, Vik SB, Tu Y. Theaflavins inhibit the ATP synthase and the respiratory chain without increasing superoxide production. J Nutr Biochem 2011; 23:953-60. [PMID: 21924889 DOI: 10.1016/j.jnutbio.2011.05.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/22/2011] [Accepted: 05/02/2011] [Indexed: 10/17/2022]
Abstract
Four dietary polyphenols, theaflavin, theaflavin-3-gallate, theaflavin-3'-gallate and theaflavin-3,3'-digallate (TF3), have been isolated from black tea, and their effects on oxidative phosphorylation and superoxide production in a model system (Escherichia coli) have been examined. The esterified theaflavins were all potent inhibitors of the membrane-bound adenosine triphosphate (ATP) synthase, inhibiting at least 90% of the activity, with IC(50) values in the range of 10-20 μM. ATP-driven proton translocation was inhibited in a similar fashion, as was the purified F(1)-ATPase, indicating that the primary site of inhibition was in the F(1) sector. Computer modeling studies supported this interpretation. All four theaflavins were also inhibitory towards the electron transport chain, whether through complex I (NDH-1) or the alternative NADH dehydrogenase (NDH-2). Inhibition of NDH-1 by TF3 appeared to be competitive with respect to NADH, and this was supported by computer modeling studies. Rates of superoxide production during NADH oxidation by each dehydrogenase were measured. Superoxide production was completely eliminated in the presence of about 15 μM TF3, suggesting that inhibition of the respiratory chain by theaflavins does not contribute to superoxide production.
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Affiliation(s)
- Bo Li
- Department of Tea Science, Zhejiang University, Hangzhou, China
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3
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Scanlon JAB, Al-Shawi MK, Nakamoto RK. A rotor-stator cross-link in the F1-ATPase blocks the rate-limiting step of rotational catalysis. J Biol Chem 2008; 283:26228-40. [PMID: 18628203 DOI: 10.1074/jbc.m804858200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The F(0)F(1)-ATP synthase couples the functions of H(+) transport and ATP synthesis/hydrolysis through the efficient transmission of energy mediated by rotation of the centrally located gamma, epsilon, and c subunits. To understand the gamma subunit role in the catalytic mechanism, we previously determined the partial rate constants and devised a minimal kinetic model for the rotational hydrolytic mode of the F(1)-ATPase enzyme that uniquely fits the pre-steady state and steady state data ( Baylis Scanlon, J. A., Al-Shawi, M. K., Le, N. P., and Nakamoto, R. K. (2007) Biochemistry 46, 8785-8797 ). Here we directly test the model using two single cysteine mutants, betaD380C and betaE381C, which can be used to reversibly inhibit rotation upon formation of a cross-link with the conserved gammaCys-87. In the pre-steady state, the gamma-beta cross-linked enzyme at high Mg.ATP conditions retained the burst of hydrolysis but was not able to release P(i). These data show that the rate-limiting rotation step, k(gamma), occurs after hydrolysis and before P(i) release. This analysis provides additional insights into how the enzyme achieves efficient coupling and implicates the betaGlu-381 residue for proper formation of the rate-limiting transition state involving gamma subunit rotation.
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Affiliation(s)
- Joanne A Baylis Scanlon
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
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4
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Penefsky HS, Cross RL. Structure and mechanism of FoF1-type ATP synthases and ATPases. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 64:173-214. [PMID: 1828930 DOI: 10.1002/9780470123102.ch4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- H S Penefsky
- Department of Biochemistry and Molecular Biology, SUNY Health Science Center, Syracuse
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5
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Sauna ZE, Nandigama K, Ambudkar SV. Multidrug resistance protein 4 (ABCC4)-mediated ATP hydrolysis: effect of transport substrates and characterization of the post-hydrolysis transition state. J Biol Chem 2004; 279:48855-64. [PMID: 15364914 DOI: 10.1074/jbc.m408849200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Multidrug resistance protein 4 (MRP4/ABCC4), transports cyclic nucleoside monophosphates, nucleoside analog drugs, chemotherapeutic agents, and prostaglandins. In this study we characterize ATP hydrolysis by human MRP4 expressed in insect cells. MRP4 hydrolyzes ATP (Km, 0.62 mm), which is inhibited by orthovanadate and beryllium fluoride. However, unlike ATPase activity of P-glycoprotein, which is equally sensitive to both inhibitors, MRP4-ATPase is more sensitive to beryllium fluoride than to orthovanadate. 8-Azido[alpha-32P]ATP binds to MRP4 (concentration for half-maximal binding approximately 3 microm) and is displaced by ATP or by its non-hydrolyzable analog AMPPNP (concentrations for half-maximal inhibition of 13.3 and 308 microm). MRP4 substrates, the prostaglandins E1 and E2, stimulate ATP hydrolysis 2- to 3-fold but do not affect the Km for ATP. Several other substrates, azidothymidine, 9-(2-phosphonylmethoxyethyl)adenine, and methotrexate do not stimulate ATP hydrolysis but inhibit prostaglandin E2-stimulated ATP hydrolysis. Although both post-hydrolysis transition states MRP4.8-azido[alpha-32P]ADP.Vi and MRP4.8-azido[alpha-32P]ADP.beryllium fluoride can be generated, nucleotide trapping is approximately 4-fold higher with beryllium fluoride. The divalent cations Mg2+ and Mn2+ support comparable levels of nucleotide binding, hydrolysis, and trapping. However, Co2+ increases 8-azido[alpha-32P]ATP binding and beryllium fluoride-induced 8-azido[alpha-32P]ADP trapping but does not support steady-state ATP hydrolysis. ADP inhibits basal and prostaglandin E2-stimulated ATP hydrolysis (concentrations for half-maximal inhibition 0.19 and 0.25 mm, respectively) and beryllium fluoride-induced 8-azido[alpha-32P]ADP trapping, whereas Pi has no effect up to 20 mm. In aggregate, our results demonstrate that MRP4 exhibits substrate-stimulated ATP hydrolysis, and we propose a kinetic scheme suggesting that ADP release from the post-hydrolysis transition state may be the rate-limiting step during the catalytic cycle.
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Affiliation(s)
- Zuben E Sauna
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892-4256, USA
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6
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Tsunoda SP, Aggeler R, Noji H, Kinosita K, Yoshida M, Capaldi RA. Observations of rotation within the F(o)F(1)-ATP synthase: deciding between rotation of the F(o)c subunit ring and artifact. FEBS Lett 2000; 470:244-8. [PMID: 10745076 DOI: 10.1016/s0014-5793(00)01336-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
F(o)F(1)-ATP synthase mediates coupling of proton flow in F(o) and ATP synthesis/hydrolysis in F(1) through rotation of central rotor subunits. A ring structure of F(o)c subunits is widely believed to be a part of the rotor. Using an attached actin filament as a probe, we have observed the rotation of the F(o)c subunit ring in detergent-solubilized F(o)F(1)-ATP synthase purified from Escherichia coli. Similar studies have been performed and reported recently [Sambongi et al. (1999) Science 286, 1722-1724]. However, in our hands this rotation has been observed only for the preparations which show poor sensitivity to dicyclohexylcarbodiimde, an F(o) inhibitor. We have found that detergents which adequately disperse the enzyme for the rotation assay also tend to transform F(o)F(1)-ATP synthase into an F(o) inhibitor-insensitive state in which F(1) can hydrolyze ATP regardless of the state of the F(o). Our results raise the important issue of whether rotation of the F(o)c ring in isolated F(o)F(1)-ATP synthase can be demonstrated unequivocally with the approach adopted here and also used by Sambongi et al.
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Affiliation(s)
- S P Tsunoda
- Research Laboratory of Resources Utilization, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Japan
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7
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Rombel I, Peters-Wendisch P, Mesecar A, Thorgeirsson T, Shin YK, Kustu S. MgATP binding and hydrolysis determinants of NtrC, a bacterial enhancer-binding protein. J Bacteriol 1999; 181:4628-38. [PMID: 10419963 PMCID: PMC103596 DOI: 10.1128/jb.181.15.4628-4638.1999] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When phosphorylated, the dimeric form of nitrogen regulatory protein C (NtrC) of Salmonella typhimurium forms a larger oligomer(s) that can hydrolyze ATP and hence activate transcription by the sigma(54)-holoenzyme form of RNA polymerase. Studies of Mg-nucleoside triphosphate binding using a filter-binding assay indicated that phosphorylation is not required for nucleotide binding but probably controls nucleotide hydrolysis per se. Studies of binding by isothermal titration calorimetry indicated that the apparent K(d) of unphosphorylated NtrC for MgATPgammaS is 100 microM at 25 degrees C, and studies by filter binding indicated that the concentration of MgATP required for half-maximal binding is 130 microM at 37 degrees C. Filter-binding studies with mutant forms of NtrC defective in ATP hydrolysis implicated two regions of its central domain directly in nucleotide binding and three additional regions in hydrolysis. All five are highly conserved among activators of sigma(54)-holoenzyme. Regions implicated in binding are the Walker A motif and the region around residues G355 to R358, which may interact with the nucleotide base. Regions implicated in nucleotide hydrolysis are residues S207 and E208, which have been proposed to lie in a region analogous to the switch I effector region of p21(ras) and other purine nucleotide-binding proteins; residue R294, which may be a catalytic residue; and residue D239, which is the conserved aspartate in the putative Walker B motif. D239 appears to play a role in binding the divalent cation essential for nucleotide hydrolysis. Electron paramagnetic resonance analysis of Mn(2+) binding indicated that the central domain of NtrC does not bind divalent cation strongly in the absence of nucleotide.
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Affiliation(s)
- I Rombel
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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8
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Weber J, Dunn SD, Senior AE. Effect of the epsilon-subunit on nucleotide binding to Escherichia coli F1-ATPase catalytic sites. J Biol Chem 1999; 274:19124-8. [PMID: 10383416 DOI: 10.1074/jbc.274.27.19124] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The influence of the epsilon-subunit on the nucleotide binding affinities of the three catalytic sites of Escherichia coli F1-ATPase was investigated, using a genetically engineered Trp probe in the adenine-binding subdomain (beta-Trp-331). The interaction between epsilon and F1 was not affected by the mutation. Kd for binding of epsilon to betaY331W mutant F1 was approximately 1 nM, and epsilon inhibited ATPase activity by 90%. The only nucleotide binding affinities that showed significant differences in the epsilon-depleted and epsilon-replete forms of the enzyme were those for MgATP and MgADP at the high-affinity catalytic site 1. Kd1(MgATP) and Kd1(MgADP) were an order of magnitude higher in the absence of epsilon than in its presence. In contrast, the binding affinities for MgATP and MgADP at sites 2 and 3 were similar in the epsilon-depleted and epsilon-replete enzymes, as were the affinities at all three sites for free ATP and ADP. Comparison of MgATP binding and hydrolysis parameters showed that in the presence as well as the absence of epsilon, Km equals Kd3. Thus, in both cases, all three catalytic binding sites have to be occupied to obtain rapid (Vmax) MgATP hydrolysis rates.
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Affiliation(s)
- J Weber
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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9
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Abstract
The structure of the core catalytic unit of ATP synthase, alpha 3 beta 3 gamma, has been determined by X-ray crystallography, revealing a roughly symmetrical arrangement of alternating alpha and beta subunits around a central cavity in which helical portions of gamma are found. A low-resolution structural model of F0, based on electron spectroscopic imaging, locates subunit a and the two copies of subunit b outside of a subunit c oligomer. The structures of individual subunits epsilon and c (largely) have been solved by NMR spectroscopy, but the oligomeric structure of c is still unknown. The structures of subunits a and delta remain undefined, that of b has not yet been defined but biochemical evidence indicates a credible model. Subunits gamma, epsilon, b, and delta are at the interface between F1 and F0; gamma epsilon complex forms one element of the stalk, interacting with c at the base and alpha and beta at the top. The locations of b and delta are less clear. Elucidation of the structure F0, of the stalk, and of the entire F1F0 remains a challenging goal.
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Affiliation(s)
- J Weber
- Department of Biochemistry, University of Rochester Medical Center, NY 14642, USA
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10
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Abstract
An X-ray structure of the F1 portion of the mitochondrial ATP synthase shows asymmetry and differences in nucleotide binding of the catalytic beta subunits that support the binding change mechanism with an internal rotation of the gamma subunit. Other structural and mutational probes of the F1 and F0 portions of the ATP synthase are reviewed, together with kinetic and other evaluations of catalytic site occupancy and behavior during hydrolysis or synthesis of ATP. Subunit function as related to proton translocation and rotational catalysis is considered. Physical demonstrations of the gamma subunit rotation have been achieved. The findings have implications for other enzymatic catalyses.
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Affiliation(s)
- P D Boyer
- Molecular Biology Institute, University of California, Los Angeles 90095-1570, USA
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11
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Weber J, Bowman C, Wilke-Mounts S, Senior AE. alpha-Aspartate 261 is a key residue in noncatalytic sites of Escherichia coli F1-ATPase. J Biol Chem 1995; 270:21045-9. [PMID: 7673131 DOI: 10.1074/jbc.270.36.21045] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
X-ray structure analysis of the noncatalytic sites of F1-ATPase revealed that residue alpha-Asp261 lies close to the Mg of bound Mg-5'-adenylyl-beta,gamma-imidodiphosphate. Here, the mutation alpha D261N was generated in Escherichia coli and combined with the alpha R365W mutation, allowing nucleotide binding at F1 noncatalytic sites to be specifically monitored by tryptophan fluorescence spectroscopy. Purified alpha D261N/alpha R365W F1-ATPase showed catalytic activity similar to wild-type. An important feature was that, without any resort to nucleotide-depletion procedures, the noncatalytic sites in purified native enzyme were already empty. Binding studies with MgATP, MgADP, and the corresponding free nucleotides led to the following conclusions. Residue alpha-Asp261 interacts with the Mg of Mg-nucleotide in noncatalytic sites and provides a large component of the binding energy (approximately 3 kcal/mol). It is the primary determinant of the preference of noncatalytic sites for Mg-nucleotide. The natural ligands at these sites in wild-type enzyme are the Mg-nucleotides and free nucleotides bind poorly. Under conditions where noncatalytic sites were empty, alpha D261N/alpha R365W F1 showed significant hydrolysis of MgATP. This established unequivocally that occupancy of noncatalytic sites by nucleotide is not required for catalysis.
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Affiliation(s)
- J Weber
- Department of Biochemistry, University of Rochester Medical Center, New York 14642, USA
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12
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Schmidt G, Senior AE. ATP-dependent inactivation of the beta-Ser339Cys mutant F1-ATPase from Escherichia coli by N-ethylmaleimide. Biochemistry 1995; 34:9694-9. [PMID: 7626639 DOI: 10.1021/bi00030a006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We introduced mutations at the highly-conserved residue Ser-339 in subunit beta of Escherichia coli F1-ATPase. The mutations beta S339Y and beta S339F abolished ATPase activity and impaired enzyme assembly. In contrast beta S339C F1 retained function to a substantial degree. N-Ethylmaleimide (NEM) at 0.2-0.3 mM inactivated beta S339C F1-ATPase by 80-95% in the presence of MgATP or MgADP but did not inactivate appreciably in absence of nucleotide or presence of EDTA. In absence of nucleotide, 0.7 mol of [14C-NEM] was incorporated into beta-subunits of 1.0 mol F1: in presence of MgATP the amount was 1.7 mol/mol, i.e. the introduced Cys residue became more accessible to reaction in the presence of MgATP. In the X-ray structure of F1 (Abrahams et al. (1994) Nature 370, 621-628) one of the catalytic nucleotide-binding domains is empty (on the "beta E subunit") and contains a cleft. Residue beta-339 lies within this cleft; the cleft does not occur in the other two beta-subunits. Our data are consistent with the conclusion that in wild-type enzyme under physiological conditions, MgATP or MgADP induce an enzyme conformation in which residue beta-Ser-339 becomes more exposed, possibly similar to the situation seen in the "beta E-subunit" in the X-ray structure.
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Affiliation(s)
- G Schmidt
- Department of Biochemistry, University of Rochester Medical Center, New York 14642, USA
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13
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Mitchell C, Oliver D. Two distinct ATP-binding domains are needed to promote protein export by Escherichia coli SecA ATPase. Mol Microbiol 1993; 10:483-97. [PMID: 7968527 DOI: 10.1111/j.1365-2958.1993.tb00921.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Six putative ATP-binding motifs of SecA protein were altered by oligonucleotide-directed mutagenesis to try to define the ATP-binding regions of this multifunctional protein. The effects of the mutations were analysed by genetic and biochemical assays. The results show that SecA contains two essential ATP-binding domains. One domain is responsible for high-affinity ATP binding and contains motifs A0 and B0, located at amino acid residues 102-109 and 198-210, respectively. A second domain is responsible for low-affinity ATP binding and contains motifs A3 and a predicted B motif located at amino acid residues 503-511 and 631-653, respectively. The ATP-binding properties of both domains were essential for SecA-dependent translocation ATPase and in vitro protein translocation activities. The significance of these findings for the mechanism of SecA-dependent protein translocation is discussed.
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Affiliation(s)
- C Mitchell
- Department of Microbiology, State University of New York at Stony Brook 11794
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14
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Weber J, Wilke-Mounts S, Lee R, Grell E, Senior A. Specific placement of tryptophan in the catalytic sites of Escherichia coli F1-ATPase provides a direct probe of nucleotide binding: maximal ATP hydrolysis occurs with three sites occupied. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(20)80703-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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15
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Dreyfus G, Williams AW, Kawagishi I, Macnab RM. Genetic and biochemical analysis of Salmonella typhimurium FliI, a flagellar protein related to the catalytic subunit of the F0F1 ATPase and to virulence proteins of mammalian and plant pathogens. J Bacteriol 1993; 175:3131-8. [PMID: 8491729 PMCID: PMC204635 DOI: 10.1128/jb.175.10.3131-3138.1993] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
FliI is a Salmonella typhimurium protein that is needed for flagellar assembly and may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. FliI shows extensive sequence similarity to the catalytic beta subunit of the F0F1 ATPase (A. P. Volger, M. Homma, V. M. Irikura, and R. M. Macnab, J. Bacteriol. 173:3564-3572, 1991). It is even more similar to the Spa47 protein of Shigella flexneri (M. M. Venkatesan, J. M. Buysse, and E. V. Oaks, J. Bacteriol. 174:1990-2001, 1992) and the HrpB6 protein of Xanthomonas campestris (S. Fenselau, I. Balbo, and U. Bonas, Mol. Plant-Microbe Interact. 5:390-396, 1992), which are believed to play a role in the export of virulence proteins. Site-directed mutagenesis of residues in FliI that correspond to catalytically important residues in the F1 beta subunit resulted in loss of flagellation, supporting the hypothesis that FliI is an ATPase. FliI was overproduced and purified almost to homogeneity. It demonstrated ATP binding but not hydrolysis. An antibody raised against FliI permitted detection of the protein in wild-type cells and an estimate of about 1,500 subunits per cell. An antibody directed against the F1 beta subunit of Escherichia coli cross-reacted with FliI, confirming that the proteins are structurally related. The relationship between three proteins involved in flagellar assembly (FliI, FlhA, and FliP) and homologs in a variety of virulence systems is discussed.
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Affiliation(s)
- G Dreyfus
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511-8148
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16
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al-Shawi M, Senior A. Characterization of the adenosine triphosphatase activity of Chinese hamster P-glycoprotein. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53597-3] [Citation(s) in RCA: 179] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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17
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Pedersen PL, Thomas PJ, Garboczi DN, Bianchet M, Amzel LM. F-type ATPases: are nucleotide domains in adenylate kinase appropriate models for nucleotide domains in ATP synthase/ATPase complexes? Ann N Y Acad Sci 1992; 671:359-65. [PMID: 1288332 DOI: 10.1111/j.1749-6632.1992.tb43809.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- P L Pedersen
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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18
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Martinez R, Shao L, Weller SK. The conserved helicase motifs of the herpes simplex virus type 1 origin-binding protein UL9 are important for function. J Virol 1992; 66:6735-46. [PMID: 1328687 PMCID: PMC240170 DOI: 10.1128/jvi.66.11.6735-6746.1992] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The UL9 gene of herpes simplex virus encodes a protein that specifically recognizes sequences within the viral origins of replication and exhibits helicase and DNA-dependent ATPase activities. The specific DNA binding domain of the UL9 protein was localized to the carboxy-terminal one-third of the molecule (H. M. Weir, J. M. Calder, and N. D. Stow, Nucleic Acids Res. 17:1409-1425, 1989). The N-terminal two-thirds of the UL9 gene contains six sequence motifs found in all members of a superfamily of DNA and RNA helicases, suggesting that this region may be important for helicase activity of UL9. In this report, we examined the functional significance of these six motifs for the UL9 protein through the introduction of site-specific mutations resulting in single amino acid substitutions of the most highly conserved residues within each motif. An in vivo complementation test was used to study the effect of each mutation on the function of the UL9 protein in viral DNA replication. In this assay, a mutant UL9 protein expressed from a transfected plasmid is used to complement a replication-deficient null mutant in the UL9 gene for the amplification of herpes simplex virus origin-containing plasmids. Mutations in five of the six conserved motifs inactivated the function of the UL9 protein in viral DNA replication, providing direct evidence for the importance of these conserved motifs. Insertion mutants resulting in the introduction of two alanines at 100-residue intervals in regions outside the conserved motifs were also constructed. Three of the insertion mutations were tolerated, whereas the other five abolished UL9 function. These data indicate that other regions of the protein, in addition to the helicase motifs, are important for function in vivo. Several mutations result in instability of the mutant products, presumably because of conformational changes in the protein. Taken together, these results suggest that UL9 is very sensitive to mutations with respect to both structure and function, perhaps reflecting its multifunctional character.
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Affiliation(s)
- R Martinez
- Department of Microbiology, University of Connecticut Health Center, Farmington 06030
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19
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Duncan TM, Cross RL. A model for the catalytic site of F1-ATPase based on analogies to nucleotide-binding domains of known structure. J Bioenerg Biomembr 1992; 24:453-61. [PMID: 1429539 DOI: 10.1007/bf00762362] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An updated topological model is constructed for the catalytic nucleotide-binding site of the F1-ATPase. The model is based on analogies to the known structures of the MgATP site on adenylate kinase and the guanine nucleotide sites on elongation factor Tu (Ef-Tu) and the ras p21 protein. Recent studies of these known nucleotide-binding domains have revealed several common functional features and similar alignment of nucleotide in their binding folds, and these are used as a framework for evaluating results of affinity labeling and mutagenesis studies of the beta subunit of F1. Several potentially important residues on beta are noted that have not yet been studied by mutagenesis or affinity labeling.
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Affiliation(s)
- T M Duncan
- Department of Biochemistry and Molecular Biology, SUNY Health Science Center, Syracuse 13210
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Avni A, Anderson JD, Holland N, Rochaix JD, Gromet-Elhanan Z, Edelman M. Tentoxin sensitivity of chloroplasts determined by codon 83 of beta subunit of proton-ATPase. Science 1992; 257:1245-7. [PMID: 1387730 DOI: 10.1126/science.1387730] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Tentoxin is a naturally occurring phytotoxic peptide that causes seedling chlorosis and arrests growth in sensitive plants and algae. In vitro, it inhibits activity of the beta subunit of the plastid proton-adenosine triphosphatase (ATPase) from sensitive species. Plastid atpB genes from six closely related, tentoxin-sensitive or -resistant Nicotiana species differ at codon 83, according to their response to the toxin: glutamate correlated with resistance and aspartate correlated with sensitivity. The genetic relevance of this site was confirmed in Chlamydomonas reinhardtii by chloroplast transformation. The alga, normally tentoxin-resistant, was rendered tentoxin-sensitive by mutagenesis of its plastid atpB gene at codon 83. Codon 83 may represent a critical site on the beta subunit that does not compete with nucleotide binding or other catalytic activities.
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Affiliation(s)
- A Avni
- Department of Plant Genetics, Weizmann Institute of Science, Rehovot, Israel
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22
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Abstract
Proton ATPases function in biological energy conversion in every known living cell. Their ubiquity and antiquity make them a prime source for evolutionary studies. There are two related families of H(+)-ATPases; while the family of F-ATPases function in eubacteria chloroplasts and mitochondria, the family of V-ATPases are present in archaebacteria and the vacuolar system of eukaryotic cells. Sequence analysis of several subunits of V- and F-ATPases revealed several of the important steps in their evolution. Moreover, these studies shed light on the evolution of the various organelles of eukaryotes and suggested some events in the evolution of the three kingdoms of eubacteria, archaebacteria and eukaryotes.
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Affiliation(s)
- N Nelson
- Roche Institute of Molecular Biology, Roche Research Center, Nutley, NJ 07110
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23
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Falson P, Leterme S, Capiau C, Boutry M. Beta subunit of mitochondrial F1-ATPase from the fission yeast. Deduced sequence of the wild type protein and identification of a mutation that increases nucleotide binding. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 200:61-7. [PMID: 1831760 DOI: 10.1111/j.1432-1033.1991.tb21048.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Schizosaccharomyces pombe nuclear gene, atp2, encoding the beta subunit of the mitochondrial ATP synthase, was sequenced and found to contain a 1575-bp open reading frame. Two adjacent transcription-initiation sites were found at positions 34 and 44 nucleotides upstream of the translation-initiation codon. The deduced polypeptide sequence was composed of 525 amino acid residues (molecular mass = 56875 Da). The mature polypeptide starts at residue 45 (molecular mass = 51,685 Da), indicating the presence of a presequence of 44 residues, presumably involved in mitochondrial targeting. The atp2 mutant B59-1 [Boutry, M. & Goffeau, A. (1982) Eur. J. Biochem. 125, 471-477] and its related revertant allele R4-3 [Jault, J. M., Di Pietro, A., Falson, P., Gautheron, D. C., Boutry, M. & Goffeau, A. (1989) Biochem. Biophys. Res. Commun. 158, 392-399] were also cloned and sequenced. A single nonsense mutation, CAG (Gln170)----TAG (stop) in mutant B59-1, became a missense mutation, TAG (stop)----TAC (Tyr) in revertant R4-3. Gln170 is located between the first and second elements belonging to the nucleotide-binding site. Its substitution by a tyrosine residue increases the enzyme affinity towards ADP, the amount of endogenous nucleotides and the apparent negative cooperativity for ATPase activity.
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Affiliation(s)
- P Falson
- Unité de Biochimie Physiologique, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
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24
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Myles GM, Hearst JE, Sancar A. Site-specific mutagenesis of conserved residues within Walker A and B sequences of Escherichia coli UvrA protein. Biochemistry 1991; 30:3824-34. [PMID: 1826850 DOI: 10.1021/bi00230a004] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
UvrA is the ATPase subunit of the DNA repair enzyme (A)BC excinuclease. The amino acid sequence of this protein has revealed, in addition to two zinc fingers, three pairs of nucleotide binding motifs each consisting of a Walker A and B sequence. We have conducted site-specific mutagenesis, ATPase kinetic analyses, and nucleotide binding equilibrium measurements to correlate these sequence motifs with activity. Replacement of the invariant Lys by Ala in the putative A sequences indicated that K37 and K646 but not K353 are involved in ATP hydrolysis. In contrast, substitution of the invariant Asp by Asn in the B sequences at positions D238, D513, or D857 had little effect on the in vivo activity of the protein. Nucleotide binding studies revealed a stoichiometry of 0.5 ADP/UvrA monomer while kinetic measurements on wild-type and mutant proteins showed that the active form of UvrA is a dimer with 2 catalytic sites which interact in a positive cooperative manner in the presence of ADP; mutagenesis of K37 but not of K646 attenuated this cooperativity. Loss of ATPase activity was about 75% in the K37A, 86% in the K646A mutant, and 95% in the K37A-K646A double mutant. These amino acid substitutions had only a marginal effect on the specific binding of UvrA to damaged DNA but drastically reduced its ability to deliver UvrB to the damage site. We find that the deficient UvrB loading activity of these mutant UvrA proteins results from their inability to associate with UvrB in the form of (UvrA)2(UvrB)1 complexes. We conclude that UvrA forms a dimer with two ATPase domains involving K37 and K646 and that the work performed by ATP hydrolysis is the delivery of UvrB to the damage site on DNA.
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Affiliation(s)
- G M Myles
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599-7260
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25
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Thermodynamic analyses of the catalytic pathway of F1-ATPase from Escherichia coli. Implications regarding the nature of energy coupling by F1-ATPases. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39579-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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26
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Shull MM, Pugh DG, Lingrel JB. Characterization of the Human Na,K-ATPase α2 Gene and Identification of Intragenic Restriction Fragment Length Polymorphisms. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)71525-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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27
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Kinetic characterization of the unisite catalytic pathway of seven β-subunit mutant F1-ATPases from Escherichia coli. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)84838-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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28
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Inatomi K, Eya S, Maeda M, Futai M. Amino Acid Sequence of the α and β Subunits of Methanosarcina barkeri ATPase Deduced from Cloned Genes. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)60411-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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29
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Al-Shawi MK, Senior AE. Complete kinetic and thermodynamic characterization of the unisite catalytic pathway of Escherichia coli F1-ATPase. Comparison with mitochondrial F1-ATPase and application to the study of mutant enzymes. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)77684-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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