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Volumn 404, Issue 1, 2010, Pages 127-137

High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism

Author keywords

Nitrile reduction; Oxidoreductase; QueF; Queuosine

Indexed keywords

7 CYANO 7 DEAZAGUANINE REDUCTASE; ASPARTIC ACID; BACTERIAL ENZYME; CYSTEINE; DIMER; FERREDOXIN; GUANINE DERIVATIVE; GUANOSINE TRIPHOSPHATE CYCLOHYDROLASE I; HISTIDINE; LIGAND; OXIDOREDUCTASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; UNCLASSIFIED DRUG;

EID: 78049445153     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.09.042     Document Type: Article
Times cited : (32)

References (36)
  • 1
    • 43049099252 scopus 로고    scopus 로고
    • An embarrassment of riches: the enzymology of RNA modification
    • Iwata-Reuyl D. An embarrassment of riches: the enzymology of RNA modification. Curr. Opin. Chem. Biol. 2008, 12:126-133.
    • (2008) Curr. Opin. Chem. Biol. , vol.12 , pp. 126-133
    • Iwata-Reuyl, D.1
  • 4
    • 0037310429 scopus 로고    scopus 로고
    • Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA
    • Iwata-Reuyl D. Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA. Bioorg. Chem. 2002, 31:24-43.
    • (2002) Bioorg. Chem. , vol.31 , pp. 24-43
    • Iwata-Reuyl, D.1
  • 5
    • 0033965439 scopus 로고    scopus 로고
    • Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of Shigella flexneri: the expression of the virF gene
    • Durand J.M., Dagberg B., Uhlin B.E., Björk G.R. Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of Shigella flexneri: the expression of the virF gene. Mol. Microbiol. 2000, 35:924-935.
    • (2000) Mol. Microbiol. , vol.35 , pp. 924-935
    • Durand, J.M.1    Dagberg, B.2    Uhlin, B.E.3    Björk, G.R.4
  • 7
    • 35848965494 scopus 로고    scopus 로고
    • Mechanistic studies of Bacillus subtilis QueF, the nitrile oxidoreductase involved in queuosine biosynthesis
    • Lee B.W.K., Van Lanen S.G., Iwata-Reuyl D. Mechanistic studies of Bacillus subtilis QueF, the nitrile oxidoreductase involved in queuosine biosynthesis. Biochemistry 2007, 46:12844-12854.
    • (2007) Biochemistry , vol.46 , pp. 12844-12854
    • Lee, B.W.K.1    Van Lanen, S.G.2    Iwata-Reuyl, D.3
  • 8
    • 33744489086 scopus 로고    scopus 로고
    • Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme
    • Swairjo M.A., Reddy R.R., Lee B., Van Lanen S.G., Brown S., de Crécy-Lagard V., et al. Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme. Acta Crystallogr. Sect. F 2005, 61:945-948.
    • (2005) Acta Crystallogr. Sect. F , vol.61 , pp. 945-948
    • Swairjo, M.A.1    Reddy, R.R.2    Lee, B.3    Van Lanen, S.G.4    Brown, S.5    de Crécy-Lagard, V.6
  • 9
    • 0034192571 scopus 로고    scopus 로고
    • Sequence and structural features of the T-fold, an original tunneling building unit
    • Colloc'h N., Poupon A., Mornon J.P. Sequence and structural features of the T-fold, an original tunneling building unit. Proteins: Struct. Funct. Genet. 2000, 39:142-154.
    • (2000) Proteins: Struct. Funct. Genet. , vol.39 , pp. 142-154
    • Colloc'h, N.1    Poupon, A.2    Mornon, J.P.3
  • 12
    • 26644444335 scopus 로고    scopus 로고
    • Novel reaction mechanism of GTP cyclohydrolase I. High-resolution X-ray crystallography of Thermus thermophilus HB8 enzyme complexed with a transition state analogue, the 8-oxoguanine derivative
    • Tanaka Y., Nakagawa N., Kuramitsu S., Yokoyama S., Masui R. Novel reaction mechanism of GTP cyclohydrolase I. High-resolution X-ray crystallography of Thermus thermophilus HB8 enzyme complexed with a transition state analogue, the 8-oxoguanine derivative. J. Biochem. 2005, 138:263-275.
    • (2005) J. Biochem. , vol.138 , pp. 263-275
    • Tanaka, Y.1    Nakagawa, N.2    Kuramitsu, S.3    Yokoyama, S.4    Masui, R.5
  • 13
    • 0017575996 scopus 로고
    • Glycosyl conformational and inductive effects on the acid catalyzed hydrolysis of purine nucleosides
    • Jordan F., Niv H. Glycosyl conformational and inductive effects on the acid catalyzed hydrolysis of purine nucleosides. Nucleic Acids Res. 1977, 4:697-709.
    • (1977) Nucleic Acids Res. , vol.4 , pp. 697-709
    • Jordan, F.1    Niv, H.2
  • 16
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997, 276:307-326.
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 18
    • 0028103275 scopus 로고
    • The CCP4 suite: programs for protein crystallography
    • Collaborative Computational Project, Number 4
    • Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D: Biol. Crystallogr. 1994, 50:760-763.
    • (1994) Acta Crystallogr. Sect. D: Biol. Crystallogr. , vol.50 , pp. 760-763
  • 20
    • 33745933955 scopus 로고    scopus 로고
    • HKL-3000: the integration of data reduction and structure solution-from diffraction images to an initial model in minutes
    • Minor W., Cymborowski M., Otwinowski Z., Chruszcz M. HKL-3000: the integration of data reduction and structure solution-from diffraction images to an initial model in minutes. Acta Crystallogr. Sect. D: Biol. Crystallogr. 2006, 62:859-866.
    • (2006) Acta Crystallogr. Sect. D: Biol. Crystallogr. , vol.62 , pp. 859-866
    • Minor, W.1    Cymborowski, M.2    Otwinowski, Z.3    Chruszcz, M.4
  • 21
    • 0030809260 scopus 로고    scopus 로고
    • WARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models
    • Perrakis A., Sixma T.K., Wilson K.S., Lamzin V.S. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. Acta Crystallogr. Sect. D: Biol. Crystallogr. 1997, 53:448-455.
    • (1997) Acta Crystallogr. Sect. D: Biol. Crystallogr. , vol.53 , pp. 448-455
    • Perrakis, A.1    Sixma, T.K.2    Wilson, K.S.3    Lamzin, V.S.4
  • 28
    • 48749137581 scopus 로고
    • Stochastic boundary conditions for molecular dynamics simulations of ST2 water
    • Brünger A., Brooks C.B., Karplus M. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett. 1984, 105:495-500.
    • (1984) Chem. Phys. Lett. , vol.105 , pp. 495-500
    • Brünger, A.1    Brooks, C.B.2    Karplus, M.3
  • 29
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics: the Langevin piston method
    • Feller S.E., Zhang Y., Pastor R.W., Brooks B.R. Constant pressure molecular dynamics: the Langevin piston method. J. Chem. Phys. 1995, 103:4613-4621.
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.2    Pastor, R.W.3    Brooks, B.R.4
  • 30
    • 0001538909 scopus 로고
    • Canonical dynamics: equilibrium phase-space distributions
    • Hoover W.G. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 1985, 31:1695-1697.
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 31
    • 33646645973 scopus 로고
    • Constant pressure equations of motion
    • Hoover W.G. Constant pressure equations of motion. Phys. Rev. A 1986, 34:2499-2500.
    • (1986) Phys. Rev. A , vol.34 , pp. 2499-2500
    • Hoover, W.G.1
  • 32
    • 0034625269 scopus 로고    scopus 로고
    • High performance computational chemistry: an overview of NWChem, a distributed parallel application
    • Kendall R.A., Apra E., Bernholdt D.E., Bylaska E.J., Dupuis M., Fann G.I., et al. High performance computational chemistry: an overview of NWChem, a distributed parallel application. Comput. Phys. Commun. 2000, 128:260-283.
    • (2000) Comput. Phys. Commun. , vol.128 , pp. 260-283
    • Kendall, R.A.1    Apra, E.2    Bernholdt, D.E.3    Bylaska, E.J.4    Dupuis, M.5    Fann, G.I.6
  • 33
    • 36949034492 scopus 로고    scopus 로고
    • Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations
    • Valiev M., Yang J., Adams J.A., Taylor S.S., Weare J.H. Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations. J. Phys. Chem. B 2007, 111:13455-13464.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 13455-13464
    • Valiev, M.1    Yang, J.2    Adams, J.A.3    Taylor, S.S.4    Weare, J.H.5
  • 34
    • 0040362704 scopus 로고    scopus 로고
    • Chemical basis for enzyme catalysis
    • Bruice T.C., Benkovic S.J. Chemical basis for enzyme catalysis. Biochemistry 2000, 39:6267-6274.
    • (2000) Biochemistry , vol.39 , pp. 6267-6274
    • Bruice, T.C.1    Benkovic, S.J.2
  • 35
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic behavior
    • Becke A.D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 1988, 38:3098-3100.
    • (1988) Phys. Rev. A , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 36
    • 26344435738 scopus 로고
    • Fully optimized contracted Gaussian basis sets for atoms Li to Kr
    • Schäfer A., Horn H., Ahlrichs R. Fully optimized contracted Gaussian basis sets for atoms Li to Kr. J. Chem. Phys. 1992, 97:2571-2577.
    • (1992) J. Chem. Phys. , vol.97 , pp. 2571-2577
    • Schäfer, A.1    Horn, H.2    Ahlrichs, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.