메뉴 건너뛰기




Volumn 277, Issue 4, 2010, Pages 1045-1057

Catalytic reaction mechanism of Pseudomonas stutzeri l-rhamnose isomerase deduced from X-ray structures

Author keywords

Catalytic mechanism; Hydride shift; L rhamnose isomerase; Rare sugar; X ray structure

Indexed keywords

ISOMERASE; MANGANESE; METAL ION; RHAMNOSE;

EID: 76149098497     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2009.07548.x     Document Type: Article
Times cited : (21)

References (37)
  • 1
    • 0008053107 scopus 로고
    • Metabolism of l-rhamnose by Escherichia coli. I. l-Rhamnose isomerase
    • Wilson DM Ajl S (1957) Metabolism of l-rhamnose by Escherichia coli. I. l-Rhamnose isomerase. J Bacteriol 73, 410 414.
    • (1957) J Bacteriol , vol.73 , pp. 410-414
    • Wilson, D.M.1    Ajl, S.2
  • 2
    • 0027254760 scopus 로고
    • Sequencing and characterization of a gene cluster encoding the enzymes for l-rhamnose metabolism in Escherichia coli
    • Moralejo P, Egan SM, Hidalgo E Aguilar J (1993) Sequencing and characterization of a gene cluster encoding the enzymes for l-rhamnose metabolism in Escherichia coli. J Bacteriol 175, 5585 5594.
    • (1993) J Bacteriol , vol.175 , pp. 5585-5594
    • Moralejo, P.1    Egan, S.M.2    Hidalgo, E.3    Aguilar, J.4
  • 3
    • 0034697988 scopus 로고    scopus 로고
    • The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution
    • Korndörfer IP, Fessner WD Matthews BW (2000) The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution. J Mol Biol 300, 917 933.
    • (2000) J Mol Biol , vol.300 , pp. 917-933
    • Korndörfer, I.P.1    Fessner, W.D.2    Matthews, B.W.3
  • 4
    • 0344813758 scopus 로고    scopus 로고
    • Isolation of an l-rhamnose isomerase-constitutive mutant of Pseudomonas sp. strain LL172: Purification and characterization of the enzyme
    • Bhuiyan SH, Itami Y Izumori K (1997) Isolation of an l-rhamnose isomerase-constitutive mutant of Pseudomonas sp. strain LL172: purification and characterization of the enzyme. J Ferment Bioeng 84, 319 323.
    • (1997) J Ferment Bioeng , vol.84 , pp. 319-323
    • Bhuiyan, S.H.1    Itami, Y.2    Izumori, K.3
  • 5
    • 2942567628 scopus 로고    scopus 로고
    • Cloning, nucleotide sequence, and overexpression of the l-rhamnose isomerase gene from Pseudomonas stutzeri in Escherichia coli
    • Leang K, Takada G, Ishimura A, Okita M Izumori K (2004) Cloning, nucleotide sequence, and overexpression of the l-rhamnose isomerase gene from Pseudomonas stutzeri in Escherichia coli. Appl Environ Microbiol 70, 3298 3304.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 3298-3304
    • Leang, K.1    Takada, G.2    Ishimura, A.3    Okita, M.4    Izumori, K.5
  • 6
    • 4444300362 scopus 로고    scopus 로고
    • Novel reactions of l-rhamnose isomerase from Pseudomonas stutzeri and its relation with d-xylose isomerase via substrate specificity
    • Leang K, Takada G, Fukai Y, Morimoto Y, Granstrom TB Izumori K (2004) Novel reactions of l-rhamnose isomerase from Pseudomonas stutzeri and its relation with d-xylose isomerase via substrate specificity. Biochim Biophys Acta 1674, 68 77.
    • (2004) Biochim Biophys Acta , vol.1674 , pp. 68-77
    • Leang, K.1    Takada, G.2    Fukai, Y.3    Morimoto, Y.4    Granstrom, T.B.5    Izumori, K.6
  • 7
    • 33846012474 scopus 로고    scopus 로고
    • The structures of l-rhamnose isomerase from Pseudomonas stutzeri in complexes with l-rhamnose and d-allose provide insights into broad substrate-specificity
    • Yoshida H, Yamada M, Ohyama Y, Takada G, Izumori K Kamitori S (2007) The structures of l-rhamnose isomerase from Pseudomonas stutzeri in complexes with l-rhamnose and d-allose provide insights into broad substrate-specificity. J Mol Biol 365, 1505 1516.
    • (2007) J Mol Biol , vol.365 , pp. 1505-1516
    • Yoshida, H.1    Yamada, M.2    Ohyama, Y.3    Takada, G.4    Izumori, K.5    Kamitori, S.6
  • 8
    • 0025974544 scopus 로고
    • A metal-mediated hydride-shift mechanism for xylose isomerase based on the 1.6 Åstreptomyces rubiginosus structures with xylitol and d-xylose
    • Whitlow M, Howard AJ, Finzel BC, Poulos TL, Winborne E Gilliland GL (1991) A metal-mediated hydride-shift mechanism for xylose isomerase based on the 1.6 ÅStreptomyces rubiginosus structures with xylitol and d-xylose. Proteins 9, 153 173.
    • (1991) Proteins , vol.9 , pp. 153-173
    • Whitlow, M.1    Howard, A.J.2    Finzel, B.C.3    Poulos, T.L.4    Winborne, E.5    Gilliland, G.L.6
  • 9
    • 0001304049 scopus 로고
    • X-ray analysis of d-xylose isomerase at 1.9 Å: NNNative enzyme in complex with substrate and with a mechanism-designed inactivator
    • Carrell HL, Glusker JP, Burger V, Manfre F, Tritsch D Biellmann JF (1989) X-ray analysis of d-xylose isomerase at 1.9 Å: native enzyme in complex with substrate and with a mechanism-designed inactivator. Proc Natl Acad Sci USA 86, 4440 4444.
    • (1989) Proc Natl Acad Sci USA , vol.86 , pp. 4440-4444
    • Carrell, H.L.1    Glusker, J.P.2    Burger, V.3    Manfre, F.4    Tritsch, D.5    Biellmann, J.F.6
  • 11
    • 0025020716 scopus 로고
    • Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by d-xylose isomerase
    • Collyer CA Blow DM (1990) Observations of reaction intermediates and the mechanism of aldose-ketose interconversion by d-xylose isomerase. Proc Natl Acad Sci USA 87, 1362 1366.
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 1362-1366
    • Collyer, C.A.1    Blow, D.M.2
  • 12
    • 0025320312 scopus 로고
    • Mechanism for aldose-ketose interconversion by d-xylose isomerase involving ring opening followed by a 1,2-hydride shift
    • Collyer CA, Henrick K Blow DM (1990) Mechanism for aldose-ketose interconversion by d-xylose isomerase involving ring opening followed by a 1,2-hydride shift. J Mol Biol 212, 211 235.
    • (1990) J Mol Biol , vol.212 , pp. 211-235
    • Collyer, C.A.1    Henrick, K.2    Blow, D.M.3
  • 13
    • 0028225131 scopus 로고
    • X-ray crystallographic structures of d-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis
    • Lavie A, Allen KN, Petsko GA Ringe D (1994) X-ray crystallographic structures of d-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis. Biochemistry 33, 5469 5480.
    • (1994) Biochemistry , vol.33 , pp. 5469-5480
    • Lavie, A.1    Allen, K.N.2    Petsko, G.A.3    Ringe, D.4
  • 14
    • 0027947080 scopus 로고
    • Modes of binding substrates and their analogues to the enzyme d-xylose isomerase
    • Carrell HL, Hoier H Glusker JP (1994) Modes of binding substrates and their analogues to the enzyme d-xylose isomerase. Acta Crystallogr Sect D 50, 113 123.
    • (1994) Acta Crystallogr Sect D , vol.50 , pp. 113-123
    • Carrell, H.L.1    Hoier, H.2    Glusker, J.P.3
  • 15
    • 0028295612 scopus 로고
    • Role of the divalent metal ion in sugar binding, ring opening, and isomerization by d-xylose isomerase: Replacement of a catalytic metal by an amino acid
    • Allen KN, Lavie A, Glasfeld A, Tanada TN, Gerrity DP, Carlson SC, Farber GK, Petsko GA Ringe D (1994) Role of the divalent metal ion in sugar binding, ring opening, and isomerization by d-xylose isomerase: replacement of a catalytic metal by an amino acid. Biochemistry 33, 1488 1494.
    • (1994) Biochemistry , vol.33 , pp. 1488-1494
    • Allen, K.N.1    Lavie, A.2    Glasfeld, A.3    Tanada, T.N.4    Gerrity, D.P.5    Carlson, S.C.6    Farber, G.K.7    Petsko, G.A.8    Ringe, D.9
  • 16
    • 2542578790 scopus 로고    scopus 로고
    • Xylose isomerase in substrate and inhibitor Michaelis states: Atomic resolution studies of a metal-mediated hydride shift
    • Fenn TD, Ringe D Petsko GA (2004) Xylose isomerase in substrate and inhibitor Michaelis states: atomic resolution studies of a metal-mediated hydride shift. Biochemistry 43, 6464 6474.
    • (2004) Biochemistry , vol.43 , pp. 6464-6474
    • Fenn, T.D.1    Ringe, D.2    Petsko, G.A.3
  • 20
    • 0028197040 scopus 로고
    • Isotopic exchange plus substrate and inhibition kinetics of d-xylose isomerase do not support a proton-transfer mechanism
    • Allen KN, Lavie A, Farber GK, Glsfeld A, Petsko GA Ringe D (1994) Isotopic exchange plus substrate and inhibition kinetics of d-xylose isomerase do not support a proton-transfer mechanism. Biochemistry 33, 1481 1487.
    • (1994) Biochemistry , vol.33 , pp. 1481-1487
    • Allen, K.N.1    Lavie, A.2    Farber, G.K.3    Glsfeld, A.4    Petsko, G.A.5    Ringe, D.6
  • 21
    • 0346814641 scopus 로고
    • A new spectrophotometric method for the detection of keto sugars and trioses
    • Dishe Z Borenfreud E (1951) A new spectrophotometric method for the detection of keto sugars and trioses. J Biol Chem 192, 583 587.
    • (1951) J Biol Chem , vol.192 , pp. 583-587
    • Dishe, Z.1    Borenfreud, E.2
  • 22
    • 0001064332 scopus 로고
    • A neutron diffraction refinement of the crystal structure of α-l-rhamnose monohydrate
    • Takagi S Jeffrey GA (1978) A neutron diffraction refinement of the crystal structure of α-l-rhamnose monohydrate. Acta Crystallogr Sect B 34, 2551 2555.
    • (1978) Acta Crystallogr Sect B , vol.34 , pp. 2551-2555
    • Takagi, S.1    Jeffrey, G.A.2
  • 25
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project 4
    • Collaborative Computational Project 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr Sect D 50, 760 763.
    • (1994) Acta Crystallogr Sect D , vol.50 , pp. 760-763
  • 26
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An automated program for molecular replacement
    • Vagin A Teplyakov A (1997) MOLREP: an automated program for molecular replacement. J Appl Crystallogr 30, 1022 1025.
    • (1997) J Appl Crystallogr , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 27
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley P Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D 60, 2126 2132.
    • (2004) Acta Crystallogr Sect D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 28
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit: A versatile program for manipulating atomic coordinate and electron density
    • McRee DE (1999) XtalView/Xfit: a versatile program for manipulating atomic coordinate and electron density. J Struct Biol 125, 156 165.
    • (1999) J Struct Biol , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 30
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov GN, Vagin AA Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr Sect D 53, 240 255.
    • (1997) Acta Crystallogr Sect D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 35
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising
    • Allen FH (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr Sect B 58, 380 388.
    • (2002) Acta Crystallogr Sect B , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 37
    • 51449118944 scopus 로고    scopus 로고
    • Fujitsu. Fujitsu Ltd. Tokyo.
    • Fujitsu (2004) WinMOPAC V3.9. Fujitsu Ltd., Tokyo.
    • (2004) WinMOPAC V3.9.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.