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Volumn 20, Issue 6, 2010, Pages 702-710

A role for flexible loops in enzyme catalysis

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CARBOXYLIC ACID; GLUTAMIC ACID; GLYCEROL 3 PHOSPHATE DEHYDROGENASE; OROTIDINE 5' PHOSPHATE DECARBOXYLASE; PHOSPHITE; SOLVENT; TRIOSEPHOSPHATE ISOMERASE; WATER;

EID: 78649649414     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2010.09.005     Document Type: Review
Times cited : (154)

References (60)
  • 1
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland D.E. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 1958, 44:98-104.
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 2
    • 0002724139 scopus 로고
    • The role of induced fit and conformational changes of enzymes in specificity and catalysis
    • Herschlag D. The role of induced fit and conformational changes of enzymes in specificity and catalysis. Biorg Chem 1988, 16:62-96.
    • (1988) Biorg Chem , vol.16 , pp. 62-96
    • Herschlag, D.1
  • 3
    • 0016624901 scopus 로고
    • Binding energy, specificity, and enzymic catalysis: the Circe effect
    • Jencks W.P. Binding energy, specificity, and enzymic catalysis: the Circe effect. Adv Enzymol Relat Areas Mol Biol 1975, 43:219-410.
    • (1975) Adv Enzymol Relat Areas Mol Biol , vol.43 , pp. 219-410
    • Jencks, W.P.1
  • 5
    • 0022971122 scopus 로고
    • Reaction energetics of a mutant triose phosphate isomerase in which the active-site glutamate has been changed to aspartate
    • Raines R.T., Sutton E.L., Straus D.R., Gilbert W., Knowles J.R. Reaction energetics of a mutant triose phosphate isomerase in which the active-site glutamate has been changed to aspartate. Biochemistry 1986, 25:7142-7154.
    • (1986) Biochemistry , vol.25 , pp. 7142-7154
    • Raines, R.T.1    Sutton, E.L.2    Straus, D.R.3    Gilbert, W.4    Knowles, J.R.5
  • 7
    • 0028296717 scopus 로고
    • Triosephosphate isomerase requires a positively charged active site: the role of lysine-12
    • Lodi P.J., Chang L.C., Knowles J.R., Komives E.A. Triosephosphate isomerase requires a positively charged active site: the role of lysine-12. Biochemistry 1994, 33:2809-2814.
    • (1994) Biochemistry , vol.33 , pp. 2809-2814
    • Lodi, P.J.1    Chang, L.C.2    Knowles, J.R.3    Komives, E.A.4
  • 8
    • 77953888039 scopus 로고    scopus 로고
    • The role of Lys-12 in catalysis by triosephosphate isomerase: a two-part substrate approach
    • Go M.K., Koudelka A., Amyes T.L., Richard J.P. The role of Lys-12 in catalysis by triosephosphate isomerase: a two-part substrate approach. Biochemistry 2010, 49:5377-5389.
    • (2010) Biochemistry , vol.49 , pp. 5377-5389
    • Go, M.K.1    Koudelka, A.2    Amyes, T.L.3    Richard, J.P.4
  • 9
    • 0037422593 scopus 로고    scopus 로고
    • Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-Å resolution
    • Jogl G., Rozovsky S., McDermott A.E., Tong L. Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-Å resolution. Proc Natl Acad Sci USA 2003, 100:50-55.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 50-55
    • Jogl, G.1    Rozovsky, S.2    McDermott, A.E.3    Tong, L.4
  • 10
    • 0025331920 scopus 로고
    • Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-Å resolution: implications for catalysis
    • Lolis E., Petsko G.A. Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-Å resolution: implications for catalysis. Biochemistry 1990, 29:6619-6625.
    • (1990) Biochemistry , vol.29 , pp. 6619-6625
    • Lolis, E.1    Petsko, G.A.2
  • 11
    • 0025882959 scopus 로고
    • Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analog of the intermediate on the reaction pathway
    • Davenport R.C., Bash P.A., Seaton B.A., Karplus M., Petsko G.A., Ringe D. Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analog of the intermediate on the reaction pathway. Biochemistry 1991, 30:5821-5826.
    • (1991) Biochemistry , vol.30 , pp. 5821-5826
    • Davenport, R.C.1    Bash, P.A.2    Seaton, B.A.3    Karplus, M.4    Petsko, G.A.5    Ringe, D.6
  • 12
    • 77953514501 scopus 로고    scopus 로고
    • Atomic Resolution crystallography of a complex of triosephosphate isomerase with a reaction intermediate analog: new insight in the proton transfer reaction mechanism
    • Alahuhta M., Wierenga R.K. Atomic Resolution crystallography of a complex of triosephosphate isomerase with a reaction intermediate analog: new insight in the proton transfer reaction mechanism. Proteins: Struct, Funct, Bioinf 2010, 78:1878-1888.
    • (2010) Proteins: Struct, Funct, Bioinf , vol.78 , pp. 1878-1888
    • Alahuhta, M.1    Wierenga, R.K.2
  • 13
    • 0028209049 scopus 로고
    • Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8-Å resolution
    • Zhang Z., Sugio S., Komives E.A., Liu K.D., Knowles J.R., Petsko G.A., Ringe D. Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8-Å resolution. Biochemistry 1994, 33:2830-2837.
    • (1994) Biochemistry , vol.33 , pp. 2830-2837
    • Zhang, Z.1    Sugio, S.2    Komives, E.A.3    Liu, K.D.4    Knowles, J.R.5    Petsko, G.A.6    Ringe, D.7
  • 14
    • 0035861072 scopus 로고    scopus 로고
    • Contribution of phosphate intrinsic binding energy to the enzymatic rate acceleration for triosephosphate isomerase
    • Amyes T.L., O'Donoghue A.C., Richard J.P. Contribution of phosphate intrinsic binding energy to the enzymatic rate acceleration for triosephosphate isomerase. J Am Chem Soc 2001, 123:11325-11326.
    • (2001) J Am Chem Soc , vol.123 , pp. 11325-11326
    • Amyes, T.L.1    O'Donoghue, A.C.2    Richard, J.P.3
  • 15
    • 0021471746 scopus 로고
    • Acid-base catalysis of the elimination and isomerization reactions of triose phosphates
    • Richard J.P. Acid-base catalysis of the elimination and isomerization reactions of triose phosphates. J Am Chem Soc 1984, 106:4926-4936.
    • (1984) J Am Chem Soc , vol.106 , pp. 4926-4936
    • Richard, J.P.1
  • 16
    • 34248548552 scopus 로고    scopus 로고
    • Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion
    • Amyes T.L., Richard J.P. Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion. Biochemistry 2007, 46:5841-5854.
    • (2007) Biochemistry , vol.46 , pp. 5841-5854
    • Amyes, T.L.1    Richard, J.P.2
  • 18
    • 0034104285 scopus 로고    scopus 로고
    • Anatomy of a proficient enzyme: the structure of orotidine 5′-monophosphate decarboxylase in the presence and absence of a potential transition state analog
    • Miller B.G., Hassell A.M., Wolfenden R., Milburn M.V., Short S.A. Anatomy of a proficient enzyme: the structure of orotidine 5′-monophosphate decarboxylase in the presence and absence of a potential transition state analog. Proc Natl Acad Sci USA 2000, 97:2011-2016.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 2011-2016
    • Miller, B.G.1    Hassell, A.M.2    Wolfenden, R.3    Milburn, M.V.4    Short, S.A.5
  • 21
    • 27844574242 scopus 로고    scopus 로고
    • Activation of orotidine 5′-monophosphate decarboxylase by phosphite dianion: the whole substrate is the sum of two parts
    • Amyes T.L., Richard J.P., Tait J.J. Activation of orotidine 5′-monophosphate decarboxylase by phosphite dianion: the whole substrate is the sum of two parts. J Am Chem Soc 2005, 127:15708-15709.
    • (2005) J Am Chem Soc , vol.127 , pp. 15708-15709
    • Amyes, T.L.1    Richard, J.P.2    Tait, J.J.3
  • 22
    • 0019407381 scopus 로고
    • On the attribution and additivity of binding energies
    • Jencks W.P. On the attribution and additivity of binding energies. Proc Natl Acad Sci USA 1981, 78:4046-4050.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 4046-4050
    • Jencks, W.P.1
  • 23
    • 43649086695 scopus 로고    scopus 로고
    • Phosphate binding energy and catalysis by small and large molecules
    • Morrow J.R., Amyes T.L., Richard J.P. Phosphate binding energy and catalysis by small and large molecules. Acc Chem Res 2008, 41:539-548.
    • (2008) Acc Chem Res , vol.41 , pp. 539-548
    • Morrow, J.R.1    Amyes, T.L.2    Richard, J.P.3
  • 25
    • 0000283648 scopus 로고
    • Perfection in enzyme catalysis: the energetics of triosephosphate isomerase
    • Knowles J.R., Albery W.J. Perfection in enzyme catalysis: the energetics of triosephosphate isomerase. Acc Chem Res 1977, 10:105-111.
    • (1977) Acc Chem Res , vol.10 , pp. 105-111
    • Knowles, J.R.1    Albery, W.J.2
  • 26
    • 0029000872 scopus 로고
    • Dynamics of the flexible loop of triose-phosphate isomerase: the loop motion is not ligand gated
    • Williams J.C., McDermott A.E. Dynamics of the flexible loop of triose-phosphate isomerase: the loop motion is not ligand gated. Biochemistry 1995, 34:8309-8319.
    • (1995) Biochemistry , vol.34 , pp. 8309-8319
    • Williams, J.C.1    McDermott, A.E.2
  • 27
    • 0035967901 scopus 로고    scopus 로고
    • The time scale of the catalytic loop motion in triosephosphate isomerase
    • Rozovsky S., McDermott A.E. The time scale of the catalytic loop motion in triosephosphate isomerase. J Mol Biol 2001, 310:259-270.
    • (2001) J Mol Biol , vol.310 , pp. 259-270
    • Rozovsky, S.1    McDermott, A.E.2
  • 28
    • 77249138171 scopus 로고    scopus 로고
    • 13C chemical shift assignments and conformational change upon ligand binding by magic-angle spinning solid-state NMR spectroscopy
    • 13C chemical shift assignments and conformational change upon ligand binding by magic-angle spinning solid-state NMR spectroscopy. J Mol Biol 2010, 397:233-248.
    • (2010) J Mol Biol , vol.397 , pp. 233-248
    • Xu, Y.1    Lorieau, J.2    McDermott, A.E.3
  • 29
    • 0035967856 scopus 로고    scopus 로고
    • Solution-state NMR investigations of triosephosphate isomerase active site loop motion: ligand release in relation to active site loop dynamics
    • Rozovsky S., Jogl G., Tong L., McDermott A.E. Solution-state NMR investigations of triosephosphate isomerase active site loop motion: ligand release in relation to active site loop dynamics. J Mol Biol 2001, 310:271-280.
    • (2001) J Mol Biol , vol.310 , pp. 271-280
    • Rozovsky, S.1    Jogl, G.2    Tong, L.3    McDermott, A.E.4
  • 30
    • 33748511877 scopus 로고    scopus 로고
    • Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase
    • Massi F., Wang C., Palmer A.G. Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase. Biochemistry 2006, 45:10787-10794.
    • (2006) Biochemistry , vol.45 , pp. 10787-10794
    • Massi, F.1    Wang, C.2    Palmer, A.G.3
  • 31
    • 0345894320 scopus 로고    scopus 로고
    • Active site loop motion in triosephosphate isomerase: T-jump relaxation spectroscopy of thermal activation
    • Desamero R., Rozovsky S., Zhadin N., McDermott A., Callender R. Active site loop motion in triosephosphate isomerase: T-jump relaxation spectroscopy of thermal activation. Biochemistry 2003, 42:2941-2951.
    • (2003) Biochemistry , vol.42 , pp. 2941-2951
    • Desamero, R.1    Rozovsky, S.2    Zhadin, N.3    McDermott, A.4    Callender, R.5
  • 35
    • 23844500381 scopus 로고    scopus 로고
    • On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium
    • Teixeira V.H., Cunha C.A., Machuqueiro M., Oliveira A.S.F., Victor B.L., Soares C.M., Baptista A.M. On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium. J Phys Chem B 2005, 109:14691-14706.
    • (2005) J Phys Chem B , vol.109 , pp. 14691-14706
    • Teixeira, V.H.1    Cunha, C.A.2    Machuqueiro, M.3    Oliveira, A.S.F.4    Victor, B.L.5    Soares, C.M.6    Baptista, A.M.7
  • 36
    • 0035451052 scopus 로고    scopus 로고
    • What are the dielectric "constants" of proteins and how to validate electrostatic models?
    • Schutz C.N., Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models?. Proteins: Struct, Funct, Genet 2001, 44:400-417.
    • (2001) Proteins: Struct, Funct, Genet , vol.44 , pp. 400-417
    • Schutz, C.N.1    Warshel, A.2
  • 37
    • 0028210137 scopus 로고
    • Crystal structure of the K12M/G15A triosephosphate isomerase double mutant and electrostatic analysis of the active site
    • Joseph-McCarthy D., Lolis E., Komives E.A., Petsko G.A. Crystal structure of the K12M/G15A triosephosphate isomerase double mutant and electrostatic analysis of the active site. Biochemistry 1994, 33:2815-2823.
    • (1994) Biochemistry , vol.33 , pp. 2815-2823
    • Joseph-McCarthy, D.1    Lolis, E.2    Komives, E.A.3    Petsko, G.A.4
  • 38
    • 0034682613 scopus 로고    scopus 로고
    • Contribution of enzyme-phosphoribosyl contacts to catalysis by orotidine 5′-phosphate decarboxylase
    • Miller B.G., Snider M.J., Short S.A., Wolfenden R. Contribution of enzyme-phosphoribosyl contacts to catalysis by orotidine 5′-phosphate decarboxylase. Biochemistry 2000, 39:8113-8118.
    • (2000) Biochemistry , vol.39 , pp. 8113-8118
    • Miller, B.G.1    Snider, M.J.2    Short, S.A.3    Wolfenden, R.4
  • 39
    • 75749143420 scopus 로고    scopus 로고
    • Activation of R235A mutant orotidine 5-monophosphate decarboxylase by the guanidinium cation: effective molarity of the cationic side chain of Arg-235
    • Barnett S.A., Amyes T.L., McKay Wood B., Gerlt J.A., Richard J.P. Activation of R235A mutant orotidine 5-monophosphate decarboxylase by the guanidinium cation: effective molarity of the cationic side chain of Arg-235. Biochemistry 2010, 49:824-826.
    • (2010) Biochemistry , vol.49 , pp. 824-826
    • Barnett, S.A.1    Amyes, T.L.2    McKay Wood, B.3    Gerlt, J.A.4    Richard, J.P.5
  • 40
    • 0008102926 scopus 로고
    • Method for determination of phosphate anion-cation association constants from phosphorus-31 chemical shifts
    • Haake P., Prigodich R.V. Method for determination of phosphate anion-cation association constants from phosphorus-31 chemical shifts. Inorg Chem 1984, 23:457-462.
    • (1984) Inorg Chem , vol.23 , pp. 457-462
    • Haake, P.1    Prigodich, R.V.2
  • 41
    • 0017393124 scopus 로고
    • Equilibrium constants for association of guanidinium and ammonium ions with oxyanions
    • Springs B., Haake P. Equilibrium constants for association of guanidinium and ammonium ions with oxyanions. Biorg Chem 1977, 6:181-190.
    • (1977) Biorg Chem , vol.6 , pp. 181-190
    • Springs, B.1    Haake, P.2
  • 42
    • 77957104394 scopus 로고    scopus 로고
    • Rescue of K12G triosphosphate isomerase by ammonium cations: the reaction of an enzyme in pieces
    • Go M.K., Amyes T.L., Richard J.P. Rescue of K12G triosphosphate isomerase by ammonium cations: the reaction of an enzyme in pieces. J Am Chem Soc 2010, 132:13525-13532.
    • (2010) J Am Chem Soc , vol.132 , pp. 13525-13532
    • Go, M.K.1    Amyes, T.L.2    Richard, J.P.3
  • 43
    • 0025015392 scopus 로고
    • Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop
    • Joseph D., Petsko G.A., Karplus M. Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. Science 1990, 249:1425-1428.
    • (1990) Science , vol.249 , pp. 1425-1428
    • Joseph, D.1    Petsko, G.A.2    Karplus, M.3
  • 44
    • 0031820040 scopus 로고    scopus 로고
    • Determination of the amino acid requirements for a protein hinge in triosephosphate isomerase
    • Sun J., Sampson N.S. Determination of the amino acid requirements for a protein hinge in triosephosphate isomerase. Protein Sci 1998, 7:1495-1505.
    • (1998) Protein Sci , vol.7 , pp. 1495-1505
    • Sun, J.1    Sampson, N.S.2
  • 46
    • 4444321214 scopus 로고    scopus 로고
    • Entropy effects on protein hinges: the reaction catalyzed by triosephosphate isomerase
    • Xiang J., Jung J.-Y., Sampson N.S. Entropy effects on protein hinges: the reaction catalyzed by triosephosphate isomerase. Biochemistry 2004, 43:11436-11445.
    • (2004) Biochemistry , vol.43 , pp. 11436-11445
    • Xiang, J.1    Jung, J.-Y.2    Sampson, N.S.3
  • 48
    • 0026782489 scopus 로고
    • Segmental motion in catalysis: investigation of a hydrogen bond critical for loop closure in the reaction of triosephosphate isomerase
    • Sampson N.S., Knowles J.R. Segmental motion in catalysis: investigation of a hydrogen bond critical for loop closure in the reaction of triosephosphate isomerase. Biochemistry 1992, 31:8488-8494.
    • (1992) Biochemistry , vol.31 , pp. 8488-8494
    • Sampson, N.S.1    Knowles, J.R.2
  • 49
    • 34249071321 scopus 로고    scopus 로고
    • Value of a hydrogen bond in triosephosphate isomerase loop motion
    • Berlow R.B., Igumenova T.I., Loria J.P. Value of a hydrogen bond in triosephosphate isomerase loop motion. Biochemistry 2007, 46:6001-6010.
    • (2007) Biochemistry , vol.46 , pp. 6001-6010
    • Berlow, R.B.1    Igumenova, T.I.2    Loria, J.P.3
  • 50
    • 66349134420 scopus 로고    scopus 로고
    • Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase
    • Wang Y., Berlow R., Loria J. Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase. Biochemistry 2009, 48:4548-4556.
    • (2009) Biochemistry , vol.48 , pp. 4548-4556
    • Wang, Y.1    Berlow, R.2    Loria, J.3
  • 51
    • 0038391137 scopus 로고
    • Monte Carlo simulation studies of the solvation of ions. 1. Acetate anion and methylammonium cation
    • Alagona G., Ghio C., Kollman P. Monte Carlo simulation studies of the solvation of ions. 1. Acetate anion and methylammonium cation. J Am Chem Soc 1986, 108:185-191.
    • (1986) J Am Chem Soc , vol.108 , pp. 185-191
    • Alagona, G.1    Ghio, C.2    Kollman, P.3
  • 52
    • 0025785056 scopus 로고
    • Refined 1.83Å structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M-ammonium sulfate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex
    • Wierenga R.K., Noble M.E.M., Vriend G., Nauche S., Hol W.G.J. Refined 1.83Å structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M-ammonium sulfate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex. J Mol Biol 1991, 220:995-1015.
    • (1991) J Mol Biol , vol.220 , pp. 995-1015
    • Wierenga, R.K.1    Noble, M.E.M.2    Vriend, G.3    Nauche, S.4    Hol, W.G.J.5
  • 53
    • 0032584261 scopus 로고    scopus 로고
    • The enhancement of enzymatic rate accelerations by Bronsted acid-base catalysis
    • Richard J.P. The enhancement of enzymatic rate accelerations by Bronsted acid-base catalysis. Biochemistry 1998, 37:4305-4309.
    • (1998) Biochemistry , vol.37 , pp. 4305-4309
    • Richard, J.P.1
  • 54
    • 0030734269 scopus 로고    scopus 로고
    • NMR studies of the role of hydrogen bonding in the mechanism of triosephosphate isomerase
    • Harris T.K., Abeygunawardana C., Mildvan A.S. NMR studies of the role of hydrogen bonding in the mechanism of triosephosphate isomerase. Biochemistry 1997, 36:14661-14675.
    • (1997) Biochemistry , vol.36 , pp. 14661-14675
    • Harris, T.K.1    Abeygunawardana, C.2    Mildvan, A.S.3
  • 55
    • 0000995427 scopus 로고    scopus 로고
    • a matching and environmental effects on the strengths of hydrogen bonds and their potential roles in enzymic catalysis
    • a matching and environmental effects on the strengths of hydrogen bonds and their potential roles in enzymic catalysis. J Org Chem 1998, 63:4611-4619.
    • (1998) J Org Chem , vol.63 , pp. 4611-4619
    • Chen, J.1    McAllister, M.A.2    Lee, J.K.3    Houk, K.N.4
  • 57
    • 0037984337 scopus 로고    scopus 로고
    • Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-Å resolution
    • Kursula I., Wierenga R.K. Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-Å resolution. J Biol Chem 2003, 278:9544-9551.
    • (2003) J Biol Chem , vol.278 , pp. 9544-9551
    • Kursula, I.1    Wierenga, R.K.2
  • 59
    • 84962448531 scopus 로고    scopus 로고
    • The planar conformation of a strained proline ring: a QM/MM study
    • Donnini S., Groenhof G., Wierenga R.K., Juffer A.H. The planar conformation of a strained proline ring: a QM/MM study. Proteins 2006, 64:700-710.
    • (2006) Proteins , vol.64 , pp. 700-710
    • Donnini, S.1    Groenhof, G.2    Wierenga, R.K.3    Juffer, A.H.4


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