메뉴 건너뛰기




Volumn 70, Issue 6, 2010, Pages 545-556

Evolutionary bases of carbohydrate recognition and substrate discrimination in the ROK protein family

Author keywords

Enzyme evolution; Repressor; ROK; Substrate specificity; Sugar kinase

Indexed keywords

PROTEIN;

EID: 77954423979     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-010-9351-1     Document Type: Article
Times cited : (35)

References (35)
  • 1
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of best-fit models of protein evolution
    • DOI 10.1093/bioinformatics/bti263
    • F Abascal R Zardoya D Posada 2005 ProtTest: selection of best-fit models of protein evolution Bioinformatics 9 2104 2105 10.1093/bioinformatics/bti263 (Pubitemid 40668057)
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 3
    • 0026673733 scopus 로고
    • The glucose kinase gene of Streptomyces coelicolor A3(2): Its nucleotide sequence, transcriptional analysis and role in glucose repression
    • 10.1111/j.1365-2958.1992.tb01463.x
    • S Angell E Schwarz MJ Bibb 1992 The glucose kinase gene of Streptomyces coelicolor A3(2): its nucleotide sequence, transcriptional analysis and role in glucose repression Mol Microbiol 19 2833 2844 10.1111/j.1365-2958.1992.tb01463.x
    • (1992) Mol Microbiol , vol.19 , pp. 2833-2844
    • Angell, S.1    Schwarz, E.2    Bibb, M.J.3
  • 4
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • 10.1093/bioinformatics/14.9.755
    • SR Eddy 1998 Profile hidden Markov models Bioinformatics 9 755 763 10.1093/bioinformatics/14.9.755
    • (1998) Bioinformatics , vol.9 , pp. 755-763
    • Eddy, S.R.1
  • 6
    • 0001289724 scopus 로고
    • Einfluss der configuration auf die Wirkung der enzyme
    • E Fischer 1894 Einfluss der configuration auf die Wirkung der enzyme Ber Dtsch Chem Ges 27 2984 2993
    • (1894) Ber Dtsch Chem Ges , vol.27 , pp. 2984-2993
    • Fischer, E.1
  • 7
    • 0014570126 scopus 로고
    • Enzymes of glucose catabolism pathways in Colletotrichum and Gloeosporium
    • 10.2307/3757635 1:CAS:528:DyaE3cXlt1Sruw%3D%3D 5352423
    • GL Greene 1969 Enzymes of glucose catabolism pathways in Colletotrichum and Gloeosporium Mycologia 61 902 914 10.2307/3757635 1:CAS:528: DyaE3cXlt1Sruw%3D%3D 5352423
    • (1969) Mycologia , vol.61 , pp. 902-914
    • Greene, G.L.1
  • 8
    • 0035069457 scopus 로고    scopus 로고
    • Iron and metal regulation in bacteria
    • DOI 10.1016/S1369-5274(00)00184-3
    • K Hantke 2001 Iron and metal regulation in bacteria Curr Opin Microbiol 4 172 177 10.1016/S1369-5274(00)00184-3 1:CAS:528:DC%2BD3MXjvVart7Y%3D 11282473 (Pubitemid 32294419)
    • (2001) Current Opinion in Microbiology , vol.4 , Issue.2 , pp. 172-177
    • Hantke, K.1
  • 9
    • 0027463380 scopus 로고
    • A new ATP-binding fold in actin, hexokinase and Hsc70
    • DOI 10.1016/0962-8924(93)90161-S
    • KC Holmes C Sander A Valencia 1993 A new ATP-binding fold in actin, hexokinase and Hsc70 Trends Cell Biol 2 53 59 10.1016/0962-8924(93)90161-S (Pubitemid 23038936)
    • (1993) Trends in Cell Biology , vol.3 , Issue.2 , pp. 53-59
    • Holmes, K.C.1    Sander, C.2    Valencia, A.3
  • 10
    • 0035078573 scopus 로고    scopus 로고
    • Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archaeon
    • DOI 10.1016/S0969-2126(01)00577-9, PII S0969212601005779
    • S Ito S Fushinobu I Yoshioka S Koga H Matsuzawa T Wakagi 2001 Structural basis for the ADP-specificity of a novel glucokinase from a hyperthermophilic archae Structure 9 205 214 10.1016/S0969-2126(01)00577-9 1:CAS:528: DC%2BD3MXisVOqsrs%3D 11286887 (Pubitemid 32245871)
    • (2001) Structure , vol.9 , Issue.3 , pp. 205-214
    • Ito, S.1    Fushinobu, S.2    Yoshioka, I.3    Koga, S.4    Matsuzawa, H.5    Wakagi, T.6
  • 11
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • DOI 10.1093/nar/gki198
    • K Katoh K Kuma H Toh T Miyata 2005 MAFFT version 5: Improvement in accuracy of multiple sequence alignment Nucleic Acids Res 33 511 518 10.1093/nar/gki198 1:CAS:528:DC%2BD2MXhtV2qsbc%3D 15661851 (Pubitemid 40360980)
    • (2005) Nucleic Acids Research , vol.33 , Issue.2 , pp. 511-518
    • Katoh, K.1    Kuma, K.-I.2    Toh, H.3    Miyata, T.4
  • 12
    • 19644383169 scopus 로고    scopus 로고
    • Hypothesis: Structures, evolution, and ancestor of glucose kinases in the hexokinase family
    • DOI 10.1263/jbb.99.320
    • S Kawai T Mukai S Mori B Mikami K Murata 2005 Hypothesis: structure, evolution, and ancestor of glucose kinases in the hexokinase family J Biosci Bioeng 4 320 330 10.1263/jbb.99.320 (Pubitemid 40740581)
    • (2005) Journal of Bioscience and Bioengineering , vol.99 , Issue.4 , pp. 320-330
    • Kawai, S.1    Mukai, T.2    Mori, S.3    Mikami, B.4    Murata, K.5
  • 13
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • 10.1073/pnas.44.2.98 1:CAS:528:DyaG1cXms1Khtw%3D%3D 16590179
    • DE Koshland Jr 1958 Application of a theory of enzyme specificity to protein synthesis Proc Natl Acad Sci USA 44 98 104 10.1073/pnas.44.2.98 1:CAS:528:DyaG1cXms1Khtw%3D%3D 16590179
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-104
    • Koshland Jr., D.E.1
  • 14
    • 0035876166 scopus 로고    scopus 로고
    • Molecular markers of serine protease evolution
    • DOI 10.1093/emboj/20.12.3036
    • MM Krem E Di Cera 2001 Molecular markers of serine protease evolution EMBO J 20 3036 3045 10.1093/emboj/20.12.3036 1:CAS:528:DC%2BD3MXltlaksbw%3D 11406580 (Pubitemid 32611991)
    • (2001) EMBO Journal , vol.20 , Issue.12 , pp. 3036-3045
    • Krem, M.M.1    Di Cera, E.2
  • 15
    • 0024414149 scopus 로고
    • Identification and sequence analysis of the Bacillus subtilis W23 xylR gene and xyl operator
    • P Kreuzer D Gärtner R Allmansberger W Hillen 1989 Identification and sequence analysis of the Bacillus subtilis W23 xylR gene and xyl operator J Bacteriol 7 3840 3845
    • (1989) J Bacteriol , vol.7 , pp. 3840-3845
    • Kreuzer, P.1    Gärtner, D.2    Allmansberger, R.3    Hillen, W.4
  • 16
    • 36749023905 scopus 로고    scopus 로고
    • Divergent evolution of function in the ROK sugar kinase superfamily: Role of enzyme loops in substrate specificity
    • DOI 10.1021/bi700924d
    • M Larion LB Moore SM Thompson BG Miller 2007 Divergent evolution of function in the ROK sugar kinase superfamily: role of enzyme loops in substrate specificity Biochemistry 46 13564 13572 10.1021/bi700924d 1:CAS:528: DC%2BD2sXht1Cktb3J 17979299 (Pubitemid 350209952)
    • (2007) Biochemistry , vol.46 , Issue.47 , pp. 13564-13572
    • Larion, M.1    Moore, L.B.2    Thompson, S.M.3    Miller, B.G.4
  • 17
    • 0025996529 scopus 로고
    • Organization and characterization of three genes involved in d-xylose catabolism in Lactobacillus pentosus
    • 10.1007/BF00290664
    • BC Lokman P van Santen JC Verdoes J Krüse RJ Leer M Posno PH Pouwels 1991 Organization and characterization of three genes involved in d-xylose catabolism in Lactobacillus pentosus Mol Gen Genet 1-2 161 169 10.1007/BF00290664
    • (1991) Mol Gen Genet , vol.12 , pp. 161-169
    • Lokman, B.C.1    Van Santen, P.2    Verdoes, J.C.3    Krüse, J.4    Leer, R.J.5    Posno, M.6    Pouwels, P.H.7
  • 18
    • 4944262604 scopus 로고    scopus 로고
    • Crystal structures of Escherichia coli ATP-dependent glucokinase and its complex with glucose
    • DOI 10.1128/JB.186.20.6915-6927.2004
    • VV Lunin Y Li JD Schrag P Iannuzzi M Cygler A Matte 2004 Crystal structure of Escherichia coli ATP-Dependent glucokinase and its complex with glucose J Bacteriol 186 6915 6927 10.1128/JB.186.20.6915-6927.2004 1:CAS:528:DC%2BD2cXptVKrtro%3D 15466045 (Pubitemid 39332131)
    • (2004) Journal of Bacteriology , vol.186 , Issue.20 , pp. 6915-6927
    • Lunin, V.V.1    Li, Y.2    Schrag, J.D.3    Iannuzzi, P.4    Cygler, M.5    Matte, A.6
  • 19
    • 11144255171 scopus 로고    scopus 로고
    • Glutathione transferase-like proteins encoded in genomes of yeasts and fungi: Insights into evolution of a multifunctional protein superfamily
    • DOI 10.1016/j.femsle.2004.10.033, PII S0378109704007797
    • S McGoldrick SM O'Sullivan D Sheehan 2005 Glutathione transferase-like proteins encoded in genomes of yeasts and fungi: insights into evolution of a multifunctional protein superfamily FEMS Microbiol Lett 242 1 12 10.1016/j.femsle.2004.10.033 1:CAS:528:DC%2BD2cXhtFGhtrrF 15621414 (Pubitemid 40038413)
    • (2005) FEMS Microbiology Letters , vol.242 , Issue.1 , pp. 1-12
    • McGoldrick, S.1    O'Sullivan, S.M.2    Sheehan, D.3
  • 20
    • 2642547483 scopus 로고    scopus 로고
    • Bacillus subtilis GlcK activity requires cysteines within a motif that discriminates microbial glucokinase into two lineages
    • 10.1186/1471-2180-4-6 15018644
    • LR Mesak FM Mesak MK Dahl 2004 Bacillus subtilis GlcK activity requires cysteines within a motif that discriminates microbial glucokinase into two lineages BMC Microbiol 4 6 10.1186/1471-2180-4-6 15018644
    • (2004) BMC Microbiol , vol.4 , pp. 6
    • Mesak, L.R.1    Mesak, F.M.2    Dahl, M.K.3
  • 21
    • 2542594077 scopus 로고    scopus 로고
    • Identifying latent enzyme activities: Substrate ambiguity within modern bacterial sugar kinases
    • DOI 10.1021/bi049424m
    • BG Miller RT Raines 2004 Identifying latent enzyme activities: substrate ambiguity within modern bacterial sugar kinases Biochemistry 43 6387 6392 10.1021/bi049424m 1:CAS:528:DC%2BD2cXjs12jtbc%3D 15157072 (Pubitemid 38697538)
    • (2004) Biochemistry , vol.43 , Issue.21 , pp. 6387-6392
    • Miller, B.G.1    Raines, R.T.2
  • 22
    • 23844503225 scopus 로고    scopus 로고
    • Reconstitution of a defunct glycolytic pathway via recruitment of ambiguous sugar kinases
    • DOI 10.1021/bi0506268
    • BG Miller RT Raines 2005 Reconstitution of a defunct glycolytic pathway via recruitment of ambiguous sugar kinases Biochemistry 44 10776 10783 10.1021/bi0506268 1:CAS:528:DC%2BD2MXmsVynsrk%3D 16086580 (Pubitemid 41153638)
    • (2005) Biochemistry , vol.44 , Issue.32 , pp. 10776-10783
    • Miller, B.G.1    Raines, R.T.2
  • 23
    • 9644307853 scopus 로고    scopus 로고
    • Crystal structure of bacterial inorganic polyphosphate/ATP- glucomannokinase: Insights into kinase evolution
    • DOI 10.1074/jbc.M408126200
    • T Mukai S Kuwai S Mori B Mikami K Murata 2004 Crystal structure of bacterial inorganic polyphosphate/ATP-glucomannokinase J Biol Chem 48 50591 50600 10.1074/jbc.M408126200 (Pubitemid 39577876)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.48 , pp. 50591-50600
    • Mukai, T.1    Kawai, S.2    Mori, S.3    Mikami, B.4    Murata, K.5
  • 24
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • 10.1006/jmbi.2000.4042
    • C Notredame DG Higgins J Heringa 2000 T-Coffee: a novel method for fast and accurate multiple sequence alignment J Mol Biol 1 205 217 10.1006/jmbi.2000.4042
    • (2000) J Mol Biol , vol.1 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 25
    • 77954427030 scopus 로고    scopus 로고
    • Empirical statistical estimates for sequence similarities searches
    • WR Pearson 1998 Empirical statistical estimates for sequence similarities searches J Mol Biol 1 40 47
    • (1998) J Mol Biol , vol.1 , pp. 40-47
    • Pearson, W.R.1
  • 26
    • 67649327176 scopus 로고    scopus 로고
    • FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix
    • 10.1093/molbev/msp077
    • MN Price PS Dehal AP Arkin 2009 FastTree: computing large minimum evolution trees with profiles instead of a distance matrix Mol Biol Evol 7 1641 1650 10.1093/molbev/msp077
    • (2009) Mol Biol Evol , vol.7 , pp. 1641-1650
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 27
    • 0036677932 scopus 로고    scopus 로고
    • A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families
    • 10.1093/bioinformatics/18.8.1116 1:CAS:528:DC%2BD38Xms1Kgu7o%3D 12176835
    • T Pupko I Pe're D Graur M Hasegawa N Friedman 2002 A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families Bioinformatics 18 1116 1123 10.1093/bioinformatics/18.8.1116 1:CAS:528:DC%2BD38Xms1Kgu7o%3D 12176835
    • (2002) Bioinformatics , vol.18 , pp. 1116-1123
    • Pupko, T.1    Pe'Re, I.2    Graur, D.3    Hasegawa, M.4    Friedman, N.5
  • 28
    • 77954427559 scopus 로고    scopus 로고
    • Rambaut A (2007) http://tree.bio.ed.ac.uk/software/figtree/
    • (2007)
    • Rambaut A1
  • 29
    • 23844532942 scopus 로고    scopus 로고
    • The crystal structure of Mlc, a global regulator of sugar metabolism in Escherichia coli
    • DOI 10.1074/jbc.M504215200
    • A Schiefner K Gerber S Seitz W Welte K Diederichs W Boos 2005 The crystal structure of Mlc, a global regulator of sugar metabolism in Escherichia coli J Biol Chem 32 29073 29079 10.1074/jbc.M504215200 (Pubitemid 41161357)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.32 , pp. 29073-29079
    • Schiefner, A.1    Gerber, K.2    Seitz, S.3    Welte, W.4    Diederichs, K.5    Boos, W.6
  • 30
    • 0025738030 scopus 로고
    • Organization, promoter analysis and transcriptional regulation of the Staphylococcus xylosus xylose utilization operon
    • C Sizemore E Buchner T Rygus C Witke F Götz W Hillen 1991 Organization, promoter analysis and transcriptional regulation of the Staphylococcus xylosus xylose utilization operon Mol Gen Genet 3 277 284
    • (1991) Mol Gen Genet , vol.3 , pp. 277-284
    • Sizemore, C.1    Buchner, E.2    Rygus, T.3    Witke, C.4    Götz, F.5    Hillen, W.6
  • 31
    • 0028598812 scopus 로고
    • The genetic data environment an expandable GUI for multiple sequence alignment
    • 1:CAS:528:DyaK2MXjvVKksLc%3D 7704666
    • SW Smith R Overbeek CR Woese W Gilbert PM Gillevet 1994 The genetic data environment an expandable GUI for multiple sequence alignment Comput Appl Biosci 10 671 675 1:CAS:528:DyaK2MXjvVKksLc%3D 7704666
    • (1994) Comput Appl Biosci , vol.10 , pp. 671-675
    • Smith, S.W.1    Overbeek, R.2    Woese, C.R.3    Gilbert, W.4    Gillevet, P.M.5
  • 32
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • DOI 10.1093/bioinformatics/btl446
    • A Stamatakis 2006 RAxML-VL-HPC: ML-based phylogenetic analyses with thousands of taxa and mixed models Bioinformatics 21 2688 2690 10.1093/bioinformatics/btl446 (Pubitemid 44642609)
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688-2690
    • Stamatakis, A.1
  • 33
    • 0028000790 scopus 로고
    • Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria
    • 10.1099/13500872-140-9-2349 1:CAS:528:DyaK2cXmsleku74%3D
    • F Titgemeyer J Reizer A Reizer MH Saier Jr 1994 Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria Microbiol 140 2349 2354 10.1099/13500872-140-9-2349 1:CAS:528:DyaK2cXmsleku74%3D
    • (1994) Microbiol , vol.140 , pp. 2349-2354
    • Titgemeyer, F.1    Reizer, J.2    Reizer, A.3    Saier Jr., M.H.4
  • 34
    • 33645507429 scopus 로고    scopus 로고
    • M-Coffee: Combining multiple sequence alignment methods with T-Coffee
    • 10.1093/nar/gkl091 1:CAS:528:DC%2BD28XjslKqtLs%3D 16556910
    • IM Wallace O O'Sullivan DG Higgins C Notredame 2006 M-Coffee: combining multiple sequence alignment methods with T-Coffee Nucleic Acids Res 34 1692 1699 10.1093/nar/gkl091 1:CAS:528:DC%2BD28XjslKqtLs%3D 16556910
    • (2006) Nucleic Acids Res , vol.34 , pp. 1692-1699
    • Wallace, I.M.1    O'Sullivan, O.2    Higgins, D.G.3    Notredame, C.4
  • 35
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • S Whelan N Goldman 2001 A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach Mol Biol Evol 5 691 699
    • (2001) Mol Biol Evol , vol.5 , pp. 691-699
    • Whelan, S.1    Goldman, N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.