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Volumn 352, Issue 2, 2005, Pages 438-454

The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis

Author keywords

Amino acid kinase family; Protein structure; Pyrimidine nucleotide biosynthesis; UMP kinase; Uridylate kinase

Indexed keywords

ACETYLGLUTAMATE KINASE; CARBAMATE KINASE; CYTIDINE PHOSPHATE; GLUTAMYL AMINOPEPTIDASE; MAGNESIUM ION; NUCLEOSIDE MONOPHOSPHATE KINASE; PHOSPHOTRANSFERASE; UNCLASSIFIED DRUG; URIDINE PHOSPHATE; URIDINE PHOSPHATE KINASE;

EID: 23944435947     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.07.045     Document Type: Article
Times cited : (52)

References (51)
  • 3
    • 17644435744 scopus 로고    scopus 로고
    • Nucleoside monophosphate kinases: Structure, mechanism, and substrate specificity
    • H.G. Yan, and M.D. Tsai Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity Advan. Enzymol. Relat. Areas Mol. Biol. 73 1999 103 134
    • (1999) Advan. Enzymol. Relat. Areas Mol. Biol. , vol.73 , pp. 103-134
    • Yan, H.G.1    Tsai, M.D.2
  • 4
    • 0028953772 scopus 로고
    • Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP
    • L. Serina, C. Blondin, E. Krin, O. Sismeiro, A. Danchin, and H. Sakamoto Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP Biochemistry 34 1995 5066 5074
    • (1995) Biochemistry , vol.34 , pp. 5066-5074
    • Serina, L.1    Blondin, C.2    Krin, E.3    Sismeiro, O.4    Danchin, A.5    Sakamoto, H.6
  • 5
    • 0011106749 scopus 로고
    • Cloning, nucleotide sequence and expression of the Escherichia coli K-12 pyrH gene encoding UMP kinase
    • J.D. Smallshaw, and R.A. Kelln Cloning, nucleotide sequence and expression of the Escherichia coli K-12 pyrH gene encoding UMP kinase Life Sci. Advan. 11 1992 59 65
    • (1992) Life Sci. Advan. , vol.11 , pp. 59-65
    • Smallshaw, J.D.1    Kelln, R.A.2
  • 6
    • 0026485123 scopus 로고
    • Identification and characterization of the smbA gene, a suppressor of the mukB null mutant of Escherichia coli
    • K. Yamanaka, T. Ogura, H. Niki, and S. Hiraga Identification and characterization of the smbA gene, a suppressor of the mukB null mutant of Escherichia coli J. Bacteriol. 174 1992 7517 7526
    • (1992) J. Bacteriol. , vol.174 , pp. 7517-7526
    • Yamanaka, K.1    Ogura, T.2    Niki, H.3    Hiraga, S.4
  • 7
    • 0037154255 scopus 로고    scopus 로고
    • A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae
    • B.J. Akerley, E.J. Rubin, V.L. Novick, K. Amaya, N. Judson, and J.J. Mekalanos A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae Proc. Natl Acad. Sci. USA 99 2002 966 971
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 966-971
    • Akerley, B.J.1    Rubin, E.J.2    Novick, V.L.3    Amaya, K.4    Judson, N.5    Mekalanos, J.J.6
  • 9
    • 0036118398 scopus 로고    scopus 로고
    • Structure of acetylglutamate kinase, a key enzyme for arginine biosynthesis and a prototype for the amino acid kinase enzyme family, during catalysis
    • S. Ramón-Maiques, A. Marina, F. Gil-Ortiz, I. Fita, and V. Rubio Structure of acetylglutamate kinase, a key enzyme for arginine biosynthesis and a prototype for the amino acid kinase enzyme family, during catalysis Structure 10 2002 329 342
    • (2002) Structure , vol.10 , pp. 329-342
    • Ramón-Maiques, S.1    Marina, A.2    Gil-Ortiz, F.3    Fita, I.4    Rubio, V.5
  • 10
    • 0032950478 scopus 로고    scopus 로고
    • Carbamate kinase: New structural machinery for making carbamoyl phosphate, the common precursor of pyrimidines and arginine
    • A. Marina, P.M. Alzari, J. Bravo, M. Uriarte, B. Barcelona, I. Fita, and V. Rubio Carbamate kinase: new structural machinery for making carbamoyl phosphate, the common precursor of pyrimidines and arginine Protein Sci. 8 1999 934 940
    • (1999) Protein Sci. , vol.8 , pp. 934-940
    • Marina, A.1    Alzari, P.M.2    Bravo, J.3    Uriarte, M.4    Barcelona, B.5    Fita, I.6    Rubio, V.7
  • 11
    • 0034595434 scopus 로고    scopus 로고
    • The 1.5 Å resolution crystal structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic Archaeon Pyrococcus furiosus, bound to ADP, confirms that this thermostable enzyme is a carbamate kinase, and provides insight into substrate binding and stability in carbamate kinases
    • S. Ramón-Maiques, A. Marina, M. Uriarte, I. Fita, and V. Rubio The 1.5 Å resolution crystal structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic Archaeon Pyrococcus furiosus, bound to ADP, confirms that this thermostable enzyme is a carbamate kinase, and provides insight into substrate binding and stability in carbamate kinases J. Mol. Biol. 299 2000 463 476
    • (2000) J. Mol. Biol. , vol.299 , pp. 463-476
    • Ramón-Maiques, S.1    Marina, A.2    Uriarte, M.3    Fita, I.4    Rubio, V.5
  • 12
    • 0043270606 scopus 로고    scopus 로고
    • UMP kinase from the Gram-positive bacterium Bacillus subtilis is strongly dependent on GTP for optimal activity
    • C. Gagyi, N. Bucurenci, O. Sîrbu, G. Labessse, M. Ionescu, and A. Ofiteru UMP kinase from the Gram-positive bacterium Bacillus subtilis is strongly dependent on GTP for optimal activity Eur. J. Biochem. 270 2003 3196 3204
    • (2003) Eur. J. Biochem. , vol.270 , pp. 3196-3204
    • Gagyi, C.1    Bucurenci, N.2    Sîrbu, O.3    Labessse, G.4    Ionescu, M.5    Ofiteru, A.6
  • 13
    • 4344705266 scopus 로고    scopus 로고
    • Structure-function relationships of UMP kinases from pyrH mutants of Gram-negative bacteria
    • H. Sakamoto, S. Landais, C. Evrin, C. Laurent-Winter, O. Barzu, and R.A. Kelln Structure-function relationships of UMP kinases from pyrH mutants of Gram-negative bacteria Microbiology 150 2004 2153 2159
    • (2004) Microbiology , vol.150 , pp. 2153-2159
    • Sakamoto, H.1    Landais, S.2    Evrin, C.3    Laurent-Winter, C.4    Barzu, O.5    Kelln, R.A.6
  • 14
    • 0242411465 scopus 로고    scopus 로고
    • Site-directed mutagenesis of Escherichia coli acetylglutamate kinase and aspartokinase III probes the catalytic and substrate-binding mechanisms of these amino acid kinase family enzymes and allows three-dimensional modelling of aspartokinase
    • C. Marco-Marín, S. Ramón-Maiques, S. Tavarez, and V. Rubio Site-directed mutagenesis of Escherichia coli acetylglutamate kinase and aspartokinase III probes the catalytic and substrate-binding mechanisms of these amino acid kinase family enzymes and allows three-dimensional modelling of aspartokinase J. Mol. Biol. 334 2003 459 476
    • (2003) J. Mol. Biol. , vol.334 , pp. 459-476
    • Marco-Marín, C.1    Ramón-Maiques, S.2    Tavarez, S.3    Rubio, V.4
  • 15
    • 21644456971 scopus 로고    scopus 로고
    • Glutamate-5-kinase from Escherichia coli: Gene cloning, overexpression, purification and crystallization of the recombinant enzyme and preliminary X-ray studies
    • I. Pérez-Arellano, F. Gil-Ortiz, J. Cervera, and V. Rubio Glutamate-5-kinase from Escherichia coli: gene cloning, overexpression, purification and crystallization of the recombinant enzyme and preliminary X-ray studies Acta Crystallog. sect. D 60 2004 2091 2094
    • (2004) Acta Crystallog. Sect. D , vol.60 , pp. 2091-2094
    • Pérez-Arellano, I.1    Gil-Ortiz, F.2    Cervera, J.3    Rubio, V.4
  • 16
    • 0016736980 scopus 로고
    • N-Acetylglutamate synthase of Escherichia coli regulation of synthesis and activity by arginine
    • T. Leisinger, and D. Haas N-Acetylglutamate synthase of Escherichia coli regulation of synthesis and activity by arginine J. Biol. Chem. 250 1975 1690 1693
    • (1975) J. Biol. Chem. , vol.250 , pp. 1690-1693
    • Leisinger, T.1    Haas, D.2
  • 17
    • 4444234384 scopus 로고    scopus 로고
    • Arginine biosynthesis in Thermotoga maritima: Characterization of the arginine-sensitive N-acetyl-l-glutamate kinase
    • M.L. Fernández-Murga, F. Gil-Ortiz, J.L. Llácer, and V. Rubio Arginine biosynthesis in Thermotoga maritima: characterization of the arginine-sensitive N-acetyl-l-glutamate kinase J. Bacteriol. 186 2004 6142 6149
    • (2004) J. Bacteriol. , vol.186 , pp. 6142-6149
    • Fernández-Murga, M.L.1    Gil-Ortiz, F.2    Llácer, J.L.3    Rubio, V.4
  • 18
    • 0017378572 scopus 로고
    • N-acetylglutamate synthase of Escherichia coli: Purification, characterization, and molecular properties
    • D.K. Marvil, and T. Leisinger N-acetylglutamate synthase of Escherichia coli: purification, characterization, and molecular properties J. Biol. Chem. 252 1977 3295 3303
    • (1977) J. Biol. Chem. , vol.252 , pp. 3295-3303
    • Marvil, D.K.1    Leisinger, T.2
  • 19
    • 0032563126 scopus 로고    scopus 로고
    • PyrH-encoded UMP-kinase directly participates in pyrimidine-specific modulation of promoter activity in Escherichia coli
    • A. Kholti, D. Charlier, D. Gigot, N. Huysveld, M. Roovers, and N. Glansdorff pyrH-encoded UMP-kinase directly participates in pyrimidine-specific modulation of promoter activity in Escherichia coli J. Mol. Biol. 280 1998 571 582
    • (1998) J. Mol. Biol. , vol.280 , pp. 571-582
    • Kholti, A.1    Charlier, D.2    Gigot, D.3    Huysveld, N.4    Roovers, M.5    Glansdorff, N.6
  • 20
    • 0344931801 scopus 로고    scopus 로고
    • X-ray structure of aminopeptidase a from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination
    • N. Strater, D.J. Sherratt, and S.D. Colloms X-ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination EMBO J. 18 1999 4513 4522
    • (1999) EMBO J. , vol.18 , pp. 4513-4522
    • Strater, N.1    Sherratt, D.J.2    Colloms, S.D.3
  • 21
    • 0030451819 scopus 로고    scopus 로고
    • Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
    • P.A. Rice, S. Yang, K. Mizuuchi, and H.A. Nash Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn Cell 87 1996 1295 1306
    • (1996) Cell , vol.87 , pp. 1295-1306
    • Rice, P.A.1    Yang, S.2    Mizuuchi, K.3    Nash, H.A.4
  • 23
    • 0030059640 scopus 로고    scopus 로고
    • Transcription of Bacillus subtilis degR is sigma D dependent and suppressed by multicopy proB through sigma D
    • M. Ogura, and T. Tanaka Transcription of Bacillus subtilis degR is sigma D dependent and suppressed by multicopy proB through sigma D J. Bacteriol. 178 1996 216 222
    • (1996) J. Bacteriol. , vol.178 , pp. 216-222
    • Ogura, M.1    Tanaka, T.2
  • 24
    • 13444259730 scopus 로고    scopus 로고
    • First-time crystallization and preliminary X-ray crystallographic analysis of a bacterial-archaeal type UMP kinase, a key enzyme in microbial pyrimidine biosynthesis
    • C. Marco-Marín, J.M. Escamilla-Honrubia, and V. Rubio First-time crystallization and preliminary X-ray crystallographic analysis of a bacterial-archaeal type UMP kinase, a key enzyme in microbial pyrimidine biosynthesis Biochim. Biophys. Acta 1747 2005 271 275
    • (2005) Biochim. Biophys. Acta , vol.1747 , pp. 271-275
    • Marco-Marín, C.1    Escamilla-Honrubia, J.M.2    Rubio, V.3
  • 26
    • 0018881742 scopus 로고
    • Enzyme-catalyzed phosphoryl transfer reactions
    • J.R. Knowles Enzyme-catalyzed phosphoryl transfer reactions Annu. Rev. Biochem. 49 1980 877 919
    • (1980) Annu. Rev. Biochem. , vol.49 , pp. 877-919
    • Knowles, J.R.1
  • 27
    • 0030724727 scopus 로고    scopus 로고
    • Mechanisms of signaling and related enzymes
    • A.S. Mildvan Mechanisms of signaling and related enzymes Proteins: Struct. Funct. Genet. 29 1997 401 416
    • (1997) Proteins: Struct. Funct. Genet. , vol.29 , pp. 401-416
    • Mildvan, A.S.1
  • 29
    • 0027184481 scopus 로고    scopus 로고
    • A general two-metal-ion mechanism for catalytic RNA
    • T.A. Steitz, and J.A. Steitz A general two-metal-ion mechanism for catalytic RNA Proc. Natl Acad. Sci. USA 90 2002 6498 6502
    • (2002) Proc. Natl Acad. Sci. USA , vol.90 , pp. 6498-6502
    • Steitz, T.A.1    Steitz, J.A.2
  • 31
    • 0032539795 scopus 로고    scopus 로고
    • The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures
    • V. Villeret, B. Clantin, C. Tricot, C. Legrain, M. Roovers, and V. Stalon The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures Proc. Natl Acad. Sci. USA 95 1998 2801 2806
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 2801-2806
    • Villeret, V.1    Clantin, B.2    Tricot, C.3    Legrain, C.4    Roovers, M.5    Stalon, V.6
  • 32
    • 15844416304 scopus 로고    scopus 로고
    • Structural properties of UMP-kinase from Escherichia coli: Modulation of protein solubility by pH and UTP
    • L. Serina, N. Bucurenci, A.M. Gilles, W.K. Surewicz, H. Fabian, and H.H. Mantsch Structural properties of UMP-kinase from Escherichia coli: modulation of protein solubility by pH and UTP Biochemistry 35 1996 7003 7011
    • (1996) Biochemistry , vol.35 , pp. 7003-7011
    • Serina, L.1    Bucurenci, N.2    Gilles, A.M.3    Surewicz, W.K.4    Fabian, H.5    Mantsch, H.H.6
  • 35
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 36
    • 21844477035 scopus 로고    scopus 로고
    • Structure of Escherichia coli UMP kinase differs from that of other NMP kinases and sheds new light on enzyme regulation
    • P. Briozzo, C. Evrin, P. Meyer, L. Assairi, N. Joly, O. Bârzu, and A.M. Gilles Structure of Escherichia coli UMP kinase differs from that of other NMP kinases and sheds new light on enzyme regulation J. Biol. Chem. 280 2005 25533 25540
    • (2005) J. Biol. Chem. , vol.280 , pp. 25533-25540
    • Briozzo, P.1    Evrin, C.2    Meyer, P.3    Assairi, L.4    Joly, N.5    Bârzu, O.6    Gilles, A.M.7
  • 37
    • 0029064088 scopus 로고
    • High-level biosynthetic substitution of methionine in proteins by its analogs 2-aminohexanoic acid, selenomethionine, telluromethionine and ethionine in Escherichia coli
    • N. Budisa, B. Steipe, P. Demange, C. Eckerskorn, J. Kellermann, and R. Huber High-level biosynthetic substitution of methionine in proteins by its analogs 2-aminohexanoic acid, selenomethionine, telluromethionine and ethionine in Escherichia coli Eur. J. Biochem. 230 1995 788 796
    • (1995) Eur. J. Biochem. , vol.230 , pp. 788-796
    • Budisa, N.1    Steipe, B.2    Demange, P.3    Eckerskorn, C.4    Kellermann, J.5    Huber, R.6
  • 38
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscilation mode
    • Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscilation mode Methods Enzymol. 276 1997 307 326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 39
    • 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 Crystallog. sect. D 50 1994 760 763
    • (1994) Acta Crystallog. Sect. D , vol.50 , pp. 760-763
  • 41
    • 0033896691 scopus 로고    scopus 로고
    • Maximum-likelihood density modification
    • T.C. Terwilliger Maximum-likelihood density modification Acta Crystallog. sect. D 56 2000 965 972
    • (2000) Acta Crystallog. Sect. D , vol.56 , pp. 965-972
    • Terwilliger, T.C.1
  • 42
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • T.A. Jones, J.-Y. Zou, S. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
    • (1991) Acta Crystallog. Sect. a , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.-Y.2    Cowan, S.3    Kjeldgaard, M.4
  • 44
  • 45
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An automated program for molecular replacement
    • A. Vagin, and A. Teplyakov MOLREP: an automated program for molecular replacement J. Appl. Crystallog. 30 1997 1022 1025
    • (1997) J. Appl. Crystallog. , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 46
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 47
    • 0033119938 scopus 로고    scopus 로고
    • Further additions to MolScript version 1.4, including reading and contouring of electron-density maps
    • R.M. Esnouf Further additions to MolScript version 1.4, including reading and contouring of electron-density maps Acta Crystallog. sect. D 55 1999 938 940
    • (1999) Acta Crystallog. Sect. D , vol.55 , pp. 938-940
    • Esnouf, R.M.1
  • 48
    • 0028057108 scopus 로고
    • Raster3D Version 2.0. a program for photorealistic molecular graphics
    • E.A. Merritt, and M.E.P. Murphy Raster3D Version 2.0. A program for photorealistic molecular graphics Acta Crystallog. sect. D 50 1994 869 873
    • (1994) Acta Crystallog. Sect. D , vol.50 , pp. 869-873
    • Merritt, E.A.1    Murphy, M.E.P.2
  • 49
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • M.F. Sanner, A.J. Olson, and J.C. Spehner Reduced surface: an efficient way to compute molecular surfaces Biopolymers 38 1996 305 320
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 50
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • A.C. Wallace, R.A. Laskowski, and J.M. Thornton LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Eng. 8 1995 127 134
    • (1995) Protein Eng. , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 51
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • B. Honig, and A. Nicholls Classical electrostatics in biology and chemistry Science 268 1995 1144 1149
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2


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