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Volumn 111, Issue 51, 2014, Pages 18231-18236

Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: Temporal order and the roles of Asp27 and Tyr100

Author keywords

Dihydrofolate reductase; Kinetic isotope effect; Mechanism; Synergism

Indexed keywords

ASPARTIC ACID; BACTERIAL ENZYME; DIHYDROFOLATE REDUCTASE; PROTON; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; TERNARY COMPLEX FACTOR; TETRAHYDROFOLIC ACID; TYROSINE;

EID: 84919934356     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1415940111     Document Type: Article
Times cited : (53)

References (45)
  • 1
    • 0023668190 scopus 로고
    • Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli
    • Fierke CA, Johnson KA, Benkovic SJ (1987) Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli. Biochemistry 26(13):4085-4092.
    • (1987) Biochemistry , vol.26 , Issue.13 , pp. 4085-4092
    • Fierke, C.A.1    Johnson, K.A.2    Benkovic, S.J.3
  • 4
    • 0022546047 scopus 로고
    • Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis
    • Howell EE, Villafranca JE, Warren MS, Oatley SJ, Kraut J (1986) Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis. Science 231(4742):1123-1128.
    • (1986) Science , vol.231 , Issue.4742 , pp. 1123-1128
    • Howell, E.E.1    Villafranca, J.E.2    Warren, M.S.3    Oatley, S.J.4    Kraut, J.5
  • 5
    • 84879301337 scopus 로고    scopus 로고
    • Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans
    • Liu CT, et al. (2013) Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans. Proc Natl Acad Sci USA 110(25):10159-10164.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.25 , pp. 10159-10164
    • Liu, C.T.1
  • 6
    • 79955972786 scopus 로고    scopus 로고
    • Effect of pH on hydride transfer by Escherichia coli dihydrofolate reductase
    • Loveridge EJ, Allemann RK (2011) Effect of pH on hydride transfer by Escherichia coli dihydrofolate reductase. ChemBioChem 12(8):1258-1262.
    • (2011) ChemBioChem , vol.12 , Issue.8 , pp. 1258-1262
    • Loveridge, E.J.1    Allemann, R.K.2
  • 7
    • 0031015737 scopus 로고    scopus 로고
    • Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence
    • Sawaya MR, Kraut J (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence. Biochemistry 36(3):586-603.
    • (1997) Biochemistry , vol.36 , Issue.3 , pp. 586-603
    • Sawaya, M.R.1    Kraut, J.2
  • 8
    • 3042660150 scopus 로고    scopus 로고
    • Structure, dynamics, and catalytic function of dihydrofolate reductase
    • Schnell JR, Dyson HJ, Wright PE (2004) Structure, dynamics, and catalytic function of dihydrofolate reductase. Ann Rev Biophys Biomol Struct 33:119-140.
    • (2004) Ann Rev Biophys Biomol Struct , vol.33 , pp. 119-140
    • Schnell, J.R.1    Dyson, H.J.2    Wright, P.E.3
  • 9
    • 84856247363 scopus 로고    scopus 로고
    • Effects of the donor-acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction
    • Stojković V, Perissinotti LL, Willmer D, Benkovic SJ, Kohen A (2012) Effects of the donor-acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction. J Am Chem Soc 134(3):1738-1745.
    • (2012) J Am Chem Soc , vol.134 , Issue.3 , pp. 1738-1745
    • Stojković, V.1    Perissinotti, L.L.2    Willmer, D.3    Benkovic, S.J.4    Kohen, A.5
  • 10
    • 0033616094 scopus 로고    scopus 로고
    • Catalytic mechanism of dihydrofolate reductase enzyme. A combined quantum-mechanical/molecular-mechanical characterization of transition state structure for the hydride transfer step
    • Castillo R, Andres J, Moliner V (1999) Catalytic mechanism of dihydrofolate reductase enzyme. A combined quantum-mechanical/molecular-mechanical characterization of transition state structure for the hydride transfer step. J Am Chem Soc 121(51):12140-12147.
    • (1999) J Am Chem Soc , vol.121 , Issue.51 , pp. 12140-12147
    • Castillo, R.1    Andres, J.2    Moliner, V.3
  • 11
    • 19944416878 scopus 로고    scopus 로고
    • Small temperature dependence of the kinetic isotope effect for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase
    • Pu J, Ma S, Gao J, Truhlar DG (2005) Small temperature dependence of the kinetic isotope effect for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase. J Phys Chem B 109(18):8551-8556.
    • (2005) J Phys Chem B , vol.109 , Issue.18 , pp. 8551-8556
    • Pu, J.1    Ma, S.2    Gao, J.3    Truhlar, D.G.4
  • 12
    • 0038298137 scopus 로고    scopus 로고
    • How dihydrofolate reductase facilitates protonation of dihydrofolate
    • Rod TH, Brooks CL III (2003) How dihydrofolate reductase facilitates protonation of dihydrofolate. J Am Chem Soc 125(29):8718-8719.
    • (2003) J Am Chem Soc , vol.125 , Issue.29 , pp. 8718-8719
    • Rod, T.H.1    Brooks, C.L.2
  • 13
    • 0037188007 scopus 로고    scopus 로고
    • Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis
    • Agarwal PK, Billeter SR, Hammes-Schiffer S (2002) Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis. J Phys Chem B 106(12):3283-3293.
    • (2002) J Phys Chem B , vol.106 , Issue.12 , pp. 3283-3293
    • Agarwal, P.K.1    Billeter, S.R.2    Hammes-Schiffer, S.3
  • 14
    • 0347567536 scopus 로고    scopus 로고
    • Catalytic mechanism of dihydrofolate reductase enzyme. A combined quantum-mechanical/molecular-mechanical characterization of the N5 protonation step
    • Ferrer S, Silla E, Tuñón I, Tuñón I, Moliner V (2003) Catalytic mechanism of dihydrofolate reductase enzyme. A combined quantum-mechanical/molecular-mechanical characterization of the N5 protonation step. J Phys Chem B 107(50):14036-14041.
    • (2003) J Phys Chem B , vol.107 , Issue.50 , pp. 14036-14041
    • Ferrer, S.1    Silla, E.2    Tuñón, I.3    Tuñón, I.4    Moliner, V.5
  • 15
    • 70349085827 scopus 로고    scopus 로고
    • Different reaction mechanisms for mesophilic and thermophilic dihydrofolate reductases
    • Loveridge EJ, Behiry EM, Swanwick RS, Allemann RK (2009) Different reaction mechanisms for mesophilic and thermophilic dihydrofolate reductases. J Am Chem Soc 131(20):6926-6927.
    • (2009) J Am Chem Soc , vol.131 , Issue.20 , pp. 6926-6927
    • Loveridge, E.J.1    Behiry, E.M.2    Swanwick, R.S.3    Allemann, R.K.4
  • 16
    • 0028305058 scopus 로고
    • Determination by Raman spectroscopy of the pKa of N5 of dihydrofolate bound to dihydrofolate reductase: Mechanistic implications
    • Chen YQ, Kraut J, Blakley RL, Callender R (1994) Determination by Raman spectroscopy of the pKa of N5 of dihydrofolate bound to dihydrofolate reductase: Mechanistic implications. Biochemistry 33(23):7021-7026.
    • (1994) Biochemistry , vol.33 , Issue.23 , pp. 7021-7026
    • Chen, Y.Q.1    Kraut, J.2    Blakley, R.L.3    Callender, R.4
  • 17
    • 0026788011 scopus 로고
    • Structure and function of alternative proton-relay mutants of dihydrofolate reductase
    • David CL, et al. (1992) Structure and function of alternative proton-relay mutants of dihydrofolate reductase. Biochemistry 31(40):9813-9822.
    • (1992) Biochemistry , vol.31 , Issue.40 , pp. 9813-9822
    • David, C.L.1
  • 18
    • 0036112608 scopus 로고    scopus 로고
    • Role of water in the catalytic cycle of E. coli dihydrofolate reductase
    • Shrimpton P, Allemann RK (2002) Role of water in the catalytic cycle of E. coli dihydrofolate reductase. Protein Sci 11(6):1442-1451.
    • (2002) Protein Sci , vol.11 , Issue.6 , pp. 1442-1451
    • Shrimpton, P.1    Allemann, R.K.2
  • 19
    • 34249823367 scopus 로고    scopus 로고
    • Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate
    • Khavrutskii IV, Price DJ, Lee J, Brooks CL III (2007) Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate. Protein Sci 16(6):1087-1100.
    • (2007) Protein Sci , vol.16 , Issue.6 , pp. 1087-1100
    • Khavrutskii, I.V.1    Price, D.J.2    Lee, J.3    Brooks, C.L.4
  • 20
    • 70349786384 scopus 로고    scopus 로고
    • Efforts toward the direct experimental characterization of enzyme microenvironments: Tyrosine100 in dihydrofolate reductase
    • Groff D, Thielges MC, Cellitti S, Schultz PG, Romesberg FE (2009) Efforts toward the direct experimental characterization of enzyme microenvironments: Tyrosine100 in dihydrofolate reductase. Angew Chem Int Ed Engl 48(19):3478-3481.
    • (2009) Angew Chem Int Ed Engl , vol.48 , Issue.19 , pp. 3478-3481
    • Groff, D.1    Thielges, M.C.2    Cellitti, S.3    Schultz, P.G.4    Romesberg, F.E.5
  • 21
    • 84904878087 scopus 로고    scopus 로고
    • Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase
    • Liu CT, et al. (2014) Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase. J Am Chem Soc 136(29):10349-10360.
    • (2014) J Am Chem Soc , vol.136 , Issue.29 , pp. 10349-10360
    • Liu, C.T.1
  • 22
    • 85056398773 scopus 로고    scopus 로고
    • Theory and practice of solvent isotope effects
    • eds Kohen A, Limbach HH (Taylor & Francis, CRC Press, Boca Raton, FL)
    • Quinn DM (2005) Theory and practice of solvent isotope effects. Isotope Effects in Chemistry and Biology, eds Kohen A, Limbach HH (Taylor & Francis, CRC Press, Boca Raton, FL), Vol 41, pp 995-1018.
    • (2005) Isotope Effects in Chemistry and Biology , vol.41 , pp. 995-1018
    • Quinn, D.M.1
  • 23
    • 0000671274 scopus 로고
    • Double isotope fractionation Test for concertedness and for transition-state dominance
    • Belasco JG, Albery WJ, Knowles JR (1983) Double isotope fractionation Test for concertedness and for transition-state dominance. J Am Chem Soc 105(8):2475-2477.
    • (1983) J Am Chem Soc , vol.105 , Issue.8 , pp. 2475-2477
    • Belasco, J.G.1    Albery, W.J.2    Knowles, J.R.3
  • 24
    • 0020492976 scopus 로고
    • Use of multiple isotope effects to determine enzyme mechanisms and intrinsic isotope effects. Malic enzyme and glucose-6-phosphate dehydrogenase
    • Hermes JD, Roeske CA, O'Leary MH, Cleland WW (1982) Use of multiple isotope effects to determine enzyme mechanisms and intrinsic isotope effects. Malic enzyme and glucose-6-phosphate dehydrogenase. Biochemistry 21(20):5106-5114.
    • (1982) Biochemistry , vol.21 , Issue.20 , pp. 5106-5114
    • Hermes, J.D.1    Roeske, C.A.2    O'Leary, M.H.3    Cleland, W.W.4
  • 25
    • 80051486812 scopus 로고    scopus 로고
    • Two parallel pathways in the kinetic sequence of the dihydrofolate reductase from Mycobacterium tuberculosis
    • Czekster CM, Vandemeulebroucke A, Blanchard JS (2011) Two parallel pathways in the kinetic sequence of the dihydrofolate reductase from Mycobacterium tuberculosis. Biochemistry 50(32):7045-7056.
    • (2011) Biochemistry , vol.50 , Issue.32 , pp. 7045-7056
    • Czekster, C.M.1    Vandemeulebroucke, A.2    Blanchard, J.S.3
  • 26
    • 82455219011 scopus 로고    scopus 로고
    • Flexibility, diversity, and cooperativity: Pillars of enzyme catalysis
    • Hammes GG, Benkovic SJ, Hammes-Schiffer S (2011) Flexibility, diversity, and cooperativity: Pillars of enzyme catalysis. Biochemistry 50(48):10422-10430.
    • (2011) Biochemistry , vol.50 , Issue.48 , pp. 10422-10430
    • Hammes, G.G.1    Benkovic, S.J.2    Hammes-Schiffer, S.3
  • 27
    • 1842830209 scopus 로고    scopus 로고
    • Tunneling and coupled motion in the Escherichia coli dihydrofolate reductase catalysis
    • Sikorski RS, et al. (2004) Tunneling and coupled motion in the Escherichia coli dihydrofolate reductase catalysis. J Am Chem Soc 126(15):4778-4779.
    • (2004) J Am Chem Soc , vol.126 , Issue.15 , pp. 4778-4779
    • Sikorski, R.S.1
  • 28
    • 1542327706 scopus 로고    scopus 로고
    • Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate
    • Zhang Z, Rajagopalan PTR, Selzer T, Benkovic SJ, Hammes GG (2004) Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate. Proc Natl Acad Sci USA 101(9):2764-2769.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.9 , pp. 2764-2769
    • Zhang, Z.1    Rajagopalan, P.T.R.2    Selzer, T.3    Benkovic, S.J.4    Hammes, G.G.5
  • 29
    • 78751501376 scopus 로고    scopus 로고
    • Kinetic and chemical mechanism of the dihydrofolate reductase from Mycobacterium tuberculosis
    • Czekster CM, Vandemeulebroucke A, Blanchard JS (2011) Kinetic and chemical mechanism of the dihydrofolate reductase from Mycobacterium tuberculosis. Biochemistry 50(3):367-375.
    • (2011) Biochemistry , vol.50 , Issue.3 , pp. 367-375
    • Czekster, C.M.1    Vandemeulebroucke, A.2    Blanchard, J.S.3
  • 30
    • 33947571437 scopus 로고
    • The deuterium isotope effect
    • Wiberg KB (1955) The deuterium isotope effect. Chem Rev 55(4):713-743.
    • (1955) Chem Rev , vol.55 , Issue.4 , pp. 713-743
    • Wiberg, K.B.1
  • 31
    • 0025076417 scopus 로고
    • Dihydrofolate reductase from Escherichia coli: Probing the role of aspartate-27 and phenylalanine-137 in enzyme conformation and the binding of NADPH
    • Dunn SM, Lanigan TM, Howell EE (1990) Dihydrofolate reductase from Escherichia coli: Probing the role of aspartate-27 and phenylalanine-137 in enzyme conformation and the binding of NADPH. Biochemistry 29(37):8569-8576.
    • (1990) Biochemistry , vol.29 , Issue.37 , pp. 8569-8576
    • Dunn, S.M.1    Lanigan, T.M.2    Howell, E.E.3
  • 32
    • 84919941276 scopus 로고    scopus 로고
    • Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography
    • Wan Q, et al. (2014) Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography. Proc Natl Acad Sci USA 111:18225-18230.
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 18225-18230
    • Wan, Q.1
  • 34
    • 33644990365 scopus 로고    scopus 로고
    • Hydrogen tunneling and protein motion in enzyme reactions
    • Hammes-Schiffer S (2006) Hydrogen tunneling and protein motion in enzyme reactions. Acc Chem Res 39(2):93-100.
    • (2006) Acc Chem Res , vol.39 , Issue.2 , pp. 93-100
    • Hammes-Schiffer, S.1
  • 35
    • 79952746514 scopus 로고    scopus 로고
    • Probing coupled motions in enzymatic hydrogen tunnelling reactions: Beyond temperature-dependence studies of kinetic isotope effects
    • eds Allemann R, Scrutton N (Royal Society of Chemistry, London, UK)
    • Hay S, Sutcliffe MJ, Scrutton N (2009) Probing coupled motions in enzymatic hydrogen tunnelling reactions: Beyond temperature-dependence studies of kinetic isotope effects. Quantum Tunnelling in Enzyme-Catalyzed Reactions, eds Allemann R, Scrutton N (Royal Society of Chemistry, London, UK), pp 199-218.
    • (2009) Quantum Tunnelling in Enzyme-Catalyzed Reactions , pp. 199-218
    • Hay, S.1    Sutcliffe, M.J.2    Scrutton, N.3
  • 36
    • 84875665271 scopus 로고    scopus 로고
    • Hydrogen tunneling links protein dynamics to enzyme catalysis
    • Klinman JP, Kohen A (2013) Hydrogen tunneling links protein dynamics to enzyme catalysis. Annu Rev Biochem 82(1):471-496.
    • (2013) Annu Rev Biochem , vol.82 , Issue.1 , pp. 471-496
    • Klinman, J.P.1    Kohen, A.2
  • 37
    • 0001387613 scopus 로고
    • Diffusion effects on rapid bimolecular chemical-reactions
    • Keizer J (1987) Diffusion effects on rapid bimolecular chemical-reactions. Chem Rev 87(1):167-180.
    • (1987) Chem Rev , vol.87 , Issue.1 , pp. 167-180
    • Keizer, J.1
  • 38
    • 34547456661 scopus 로고    scopus 로고
    • Origin of the temperature dependence of isotope effects in enzymatic reactions: The case of dihydrofolate reductase
    • Liu H, Warshel A (2007) Origin of the temperature dependence of isotope effects in enzymatic reactions: The case of dihydrofolate reductase. J Phys Chem B 111(27):7852-7861.
    • (2007) J Phys Chem B , vol.111 , Issue.27 , pp. 7852-7861
    • Liu, H.1    Warshel, A.2
  • 39
    • 0031443372 scopus 로고    scopus 로고
    • Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant
    • Cameron CE, Benkovic SJ (1997) Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant. Biochemistry 36(50):15792-15800.
    • (1997) Biochemistry , vol.36 , Issue.50 , pp. 15792-15800
    • Cameron, C.E.1    Benkovic, S.J.2
  • 40
    • 84890417015 scopus 로고    scopus 로고
    • Preservation of protein dynamics in dihydrofolate reductase evolution
    • Francis K, Stojkovic V, Kohen A (2013) Preservation of protein dynamics in dihydrofolate reductase evolution. J Biol Chem 288(50):35961-35968.
    • (2013) J Biol Chem , vol.288 , Issue.50 , pp. 35961-35968
    • Francis, K.1    Stojkovic, V.2    Kohen, A.3
  • 41
    • 79960492493 scopus 로고    scopus 로고
    • Triple isotopic labeling and kinetic isotope effects: Exposing H-transfer steps in enzymatic systems
    • Sen A, Yahashiri A, Kohen A (2011) Triple isotopic labeling and kinetic isotope effects: Exposing H-transfer steps in enzymatic systems. Biochemistry 50(29):6462-6468.
    • (2011) Biochemistry , vol.50 , Issue.29 , pp. 6462-6468
    • Sen, A.1    Yahashiri, A.2    Kohen, A.3
  • 43
    • 84904130280 scopus 로고    scopus 로고
    • Practical aspects of free-energy calculations: A review
    • Hansen N, van Gunsteren WF (2014) Practical aspects of free-energy calculations: A review. J Chem Theory Comput 10(7):2632-2647.
    • (2014) J Chem Theory Comput , vol.10 , Issue.7 , pp. 2632-2647
    • Hansen, N.1    Van Gunsteren, W.F.2
  • 44
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3):435-447.
    • (2008) J Chem Theory Comput , vol.4 , Issue.3 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 45
    • 5244304444 scopus 로고
    • Efficient estimation of free-energy differences from Monte-Carlo data
    • Bennett CH (1976) Efficient estimation of free-energy differences from Monte-Carlo data. J Comput Phys 22(2):245-268.
    • (1976) J Comput Phys , vol.22 , Issue.2 , pp. 245-268
    • Bennett, C.H.1


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