메뉴 건너뛰기




Volumn 7, Issue 8, 1999, Pages 997-1008

A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase

Author keywords

B12 enzyme; Diol dehydratase; Radicals; Reaction mechanism; TIM barrel

Indexed keywords

ALDEHYDE; CARBON; COBALAMIN; COBALT; COBAMAMIDE; CYANOCOBALAMIN; HYDROLYASE; HYDROXYL GROUP; POTASSIUM ION; PROPYLENE GLYCOL; POTASSIUM; PROPANEDIOL DEHYDRATASE;

EID: 0033567082     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80126-9     Document Type: Article
Times cited : (220)

References (46)
  • 1
    • 0000102239 scopus 로고
    • 12-dependent isozymes
    • Sigel, H., & Sigel, A., eds. Marcel Dekker, Basel
    • 12-dependent isozymes. In Metal Ions in Biological Systems (Sigel, H., & Sigel, A., eds.), Vol. 30, pp. 217-254. Marcel Dekker, Basel.
    • (1994) Metal Ions in Biological Systems , vol.30 , pp. 217-254
    • Toraya, T.1
  • 2
    • 0028295773 scopus 로고
    • 12 ethanolamine ammonia lyase: Evidence for a radical mechanism
    • 12 ethanolamine ammonia lyase: Evidence for a radical mechanism. Science 263, 958-960.
    • (1994) Science , vol.263 , pp. 958-960
    • Harkins, T.T.1    Grissom, C.B.2
  • 3
    • 0032175332 scopus 로고    scopus 로고
    • The function of adenosylcobalamin in the mechanism of ribonucleoside triphosphate reductase from Lactobacillus leichmannii
    • Lawrence, C.C. & Stubbe, J. (1998). The function of adenosylcobalamin in the mechanism of ribonucleoside triphosphate reductase from Lactobacillus leichmannii. Curr. Opin. Chem. Biol. 2, 650-655.
    • (1998) Curr. Opin. Chem. Biol. , vol.2 , pp. 650-655
    • Lawrence, C.C.1    Stubbe, J.2
  • 4
    • 0002250924 scopus 로고    scopus 로고
    • 12-dependent enzymes and their models
    • Kraeutler, B., Arigoni, D., & Golding, B.T., eds. Wiley-VCH, Weinheim
    • 12-proteins (Kraeutler, B., Arigoni, D., & Golding, B.T., eds.), pp. 273-288. Wiley-VCH, Weinheim.
    • (1998) 12-proteins , pp. 273-288
    • Retey, J.1
  • 6
    • 0001129712 scopus 로고    scopus 로고
    • Cobalamin-dependent methionine synthase from Escherichia coli: Structure and reactivity
    • Kraeutler, B., Arigoni, D., & Golding, B.T., eds. Wiley-VCH, Weinheim
    • 12-proteins. (Kraeutler, B., Arigoni, D., & Golding, B.T., eds.), pp. 133-155. Wiley-VCH, Weinheim.
    • (1998) 12-proteins , pp. 133-155
    • Drennan, C.L.1    Ludwig, M.L.2
  • 8
    • 0030584657 scopus 로고    scopus 로고
    • 12 radicals are generated: The crystal structure of methylmalonyl-coenzyme A mutase at 2 Å resolution
    • 12 radicals are generated: The crystal structure of methylmalonyl-coenzyme A mutase at 2 Å resolution. Structure 4, 339-350.
    • (1996) Structure , vol.4 , pp. 339-350
    • Mancia, F.1    Evans, P.R.2
  • 9
    • 0032526407 scopus 로고    scopus 로고
    • Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism
    • Mancia, F. & Evans, P.R. (1997). Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism. Structure 6, 711-720.
    • (1997) Structure , vol.6 , pp. 711-720
    • Mancia, F.1    Evans, P.R.2
  • 12
    • 0025114388 scopus 로고
    • Evidence for a super-reduced cobamide as the major corrinoid fraction in vivo and a histidine residue as a cobalt ligand of the p-cresolyl cobamide in the acetogenic bacterium Sporomusa ovata
    • Stupperich, E., Eisinger, H.J. & Albracht, S.P.J. (1990). Evidence for a super-reduced cobamide as the major corrinoid fraction in vivo and a histidine residue as a cobalt ligand of the p-cresolyl cobamide in the acetogenic bacterium Sporomusa ovata. Eur. J. Biochem. 193, 105-109.
    • (1990) Eur. J. Biochem. , vol.193 , pp. 105-109
    • Stupperich, E.1    Eisinger, H.J.2    Albracht, S.P.J.3
  • 13
    • 0028345427 scopus 로고
    • 12-dependent 2-methyleneglutarate mutase from Clostridium barkeri in Escherichia coli
    • 12-dependent 2-methyleneglutarate mutase from Clostridium barkeri in Escherichia coli. Eur. J. Biochem. 221, 101-109.
    • (1994) Eur. J. Biochem. , vol.221 , pp. 101-109
    • Beatrix, B.1    Zelder, O.2    Linder, D.3    Buckel, W.4
  • 14
    • 0028940307 scopus 로고
    • Molecular cloning, sequencing, and expression of the genes encoding adenosylcobalamin-dependent diol dehydrase of Klebsiella oxytoca
    • Tobimatsu, T., et al., & Toraya, T. (1995). Molecular cloning, sequencing, and expression of the genes encoding adenosylcobalamin-dependent diol dehydrase of Klebsiella oxytoca. J. Biol. Chem. 270, 7142-7148.
    • (1995) J. Biol. Chem. , vol.270 , pp. 7142-7148
    • Tobimatsu, T.1    Toraya, T.2
  • 15
    • 0029841095 scopus 로고    scopus 로고
    • Cloning, sequencing, and high level expression of the genes encoding adenosylcobalamin-dependent glycerol dehydrase of Klebsiella pneumoniae
    • Tobimatsu, T., et al., & Toraya, T. (1996). Cloning, sequencing, and high level expression of the genes encoding adenosylcobalamin-dependent glycerol dehydrase of Klebsiella pneumoniae. J. Biol. Chem. 271, 22352-22357.
    • (1996) J. Biol. Chem. , vol.271 , pp. 22352-22357
    • Tobimatsu, T.1    Toraya, T.2
  • 16
    • 0025286022 scopus 로고
    • Cloning, sequencing, and expression of the genes encoding the adenosylcobalamin-dependent ethanolamine ammonia-lyase of Salmonella typhimurium
    • Faust, L.R.P., Connor, J.A., Roof, D.M., Hoch, J.A. & Babior, B.M. (1990). Cloning, sequencing, and expression of the genes encoding the adenosylcobalamin-dependent ethanolamine ammonia-lyase of Salmonella typhimurium. J. Biol. Chem. 265, 12462-12466.
    • (1990) J. Biol. Chem. , vol.265 , pp. 12462-12466
    • Faust, L.R.P.1    Connor, J.A.2    Roof, D.M.3    Hoch, J.A.4    Babior, B.M.5
  • 17
    • 0027292415 scopus 로고
    • Cloning, sequencing, and expression of the adenosylcobalamin-dependent ribonucleotide reductase from Lactobacillus leichmannii
    • Booker, S. & Stubbe, J. (1993). Cloning, sequencing, and expression of the adenosylcobalamin-dependent ribonucleotide reductase from Lactobacillus leichmannii. Proc. Natl Acad. Sci. USA 90, 8352-8356.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 8352-8356
    • Booker, S.1    Stubbe, J.2
  • 18
    • 0032492687 scopus 로고    scopus 로고
    • Evidence for axial coordination of 5,6-dimethylbenzimidazole to the cobalt atom of adenosylcobalamin bound to diol dehydratase
    • Yamanishi, M., et al., & Toraya, T. (1998). Evidence for axial coordination of 5,6-dimethylbenzimidazole to the cobalt atom of adenosylcobalamin bound to diol dehydratase. Biochemistry 37, 4799-4803.
    • (1998) Biochemistry , vol.37 , pp. 4799-4803
    • Yamanishi, M.1    Toraya, T.2
  • 19
    • 0031925224 scopus 로고    scopus 로고
    • Diol dehydratase binds coenzyme B12 in the "base-on" mode: ESR investigations on cob(II)alamin
    • Abend, A., Nitsche, R., Bandarian, V., Stupperich, E. & Retey, J. (1998). Diol dehydratase binds coenzyme B12 in the "base-on" mode: ESR investigations on cob(II)alamin. Angew. Chem. Int. Ed. Engl. 37, 625-627.
    • (1998) Angew. Chem. Int. Ed. Engl. , vol.37 , pp. 625-627
    • Abend, A.1    Nitsche, R.2    Bandarian, V.3    Stupperich, E.4    Retey, J.5
  • 21
    • 0031282402 scopus 로고    scopus 로고
    • Heterologous expression, purification, and properties of diol dehydratase, an adenosylcobalamin-dependent enzyme of Klebsiella oxytoca
    • Tobimatsu, T., et al., & Toraya, T. (1997). Heterologous expression, purification, and properties of diol dehydratase, an adenosylcobalamin-dependent enzyme of Klebsiella oxytoca. Arch. Biochem. Biophys. 347, 132-140.
    • (1997) Arch. Biochem. Biophys. , vol.347 , pp. 132-140
    • Tobimatsu, T.1    Toraya, T.2
  • 22
    • 0016140285 scopus 로고
    • 12 dependent diol dehydrase system. Dissociation of the enzyme into two different protein components and some properties of the components
    • 12 dependent diol dehydrase system. Dissociation of the enzyme into two different protein components and some properties of the components. Biochemistry 13, 3895-3899.
    • (1974) Biochemistry , vol.13 , pp. 3895-3899
    • Toraya, T.1    Uesaka, M.2    Fukui, S.3
  • 24
    • 0001957032 scopus 로고
    • 12 and cobaloximes
    • Dolphin, D., ed. John Wiley & Sons, New York
    • 12 (Dolphin, D., ed.), Vol. I, pp. 23-128. John Wiley & Sons, New York.
    • (1982) 12 , vol.1 , pp. 23-128
    • Glusker, J.P.1
  • 26
    • 0027400792 scopus 로고
    • Adenosylcobinamide methyl phosphate as a pseudocoenzyme for diol dehydrase
    • Ishida, A. & Toraya, T. (1993). Adenosylcobinamide methyl phosphate as a pseudocoenzyme for diol dehydrase. Biochemistry 32, 1535-1540.
    • (1993) Biochemistry , vol.32 , pp. 1535-1540
    • Ishida, A.1    Toraya, T.2
  • 27
    • 0027585115 scopus 로고
    • Importance of the nucleotide loop moiety coordinated to the cobalt atom of adenosylcobalamin for coenzymic function in the diol dehydrase reaction
    • Ishida, A., Ichikawa, M., Kobayashi, K., Hitomi, T., Kojima, S. & Toraya, T. (1993). Importance of the nucleotide loop moiety coordinated to the cobalt atom of adenosylcobalamin for coenzymic function in the diol dehydrase reaction. J. Nutr. Sci. Vitaminol. 39, 115-125.
    • (1993) J. Nutr. Sci. Vitaminol. , vol.39 , pp. 115-125
    • Ishida, A.1    Ichikawa, M.2    Kobayashi, K.3    Hitomi, T.4    Kojima, S.5    Toraya, T.6
  • 28
    • 0017575198 scopus 로고
    • Mechanism of action of adenosylcobalamin: Glycerol and other substrate analogues as substrates and inactivators for propanediol dehydratase-kinetics, stereospecificity, and mechanism
    • Bachovchin, W.W., Eagar, R.G., Jr., Moore, K.W. & Richards, J.H. (1977). Mechanism of action of adenosylcobalamin: Glycerol and other substrate analogues as substrates and inactivators for propanediol dehydratase-kinetics, stereospecificity, and mechanism. Biochemistry 16, 1082-1092.
    • (1977) Biochemistry , vol.16 , pp. 1082-1092
    • Bachovchin, W.W.1    Eagar R.G., Jr.2    Moore, K.W.3    Richards, J.H.4
  • 30
    • 73649177916 scopus 로고
    • Purification and properties of diol dehydratase, an enzyme requiring a cobamide coenzyme
    • Lee, H.A., Jr., & Abeles, R.H. (1963). Purification and properties of diol dehydratase, an enzyme requiring a cobamide coenzyme. J. Biol. Chem. 238, 2367-2373.
    • (1963) J. Biol. Chem. , vol.238 , pp. 2367-2373
    • Lee H.A., Jr.1    Abeles, R.H.2
  • 33
    • 0000198545 scopus 로고
    • 12 coenzyme: Theory and models
    • Dolphin, D., ed. John Wiley & Sons, New York
    • 12 (Dolphin, D., ed.), Vol. I, pp. 543-582. John Wiley & Sons, New York.
    • (1982) 12 , vol.1 , pp. 543-582
    • Golding, B.T.1
  • 34
    • 0017171488 scopus 로고
    • On the mechanism of action of adenosylcobalamin
    • Golding, B.T. & Radom, L. (1976). On the mechanism of action of adenosylcobalamin. J. Am. Chem.Soc. 98, 6331-6338.
    • (1976) J. Am. Chem.Soc. , vol.98 , pp. 6331-6338
    • Golding, B.T.1    Radom, L.2
  • 35
    • 33847805540 scopus 로고
    • Acid-base properties of free radicals in solution
    • Hayon, E. & Simic, M. (1974). Acid-base properties of free radicals in solution. Acc. Chem. Res. 7, 114-121.
    • (1974) Acc. Chem. Res. , vol.7 , pp. 114-121
    • Hayon, E.1    Simic, M.2
  • 36
    • 0002295038 scopus 로고    scopus 로고
    • 12-dependent carbon-carbon and carbon-oxygen rearrangements
    • Kraeutler, B., Arigoni, D. & Golding, B.T. eds. Wiley-VCH, Weinheim
    • 12-proteins (Kraeutler, B., Arigoni, D. & Golding, B.T. eds.), pp. 237-251. Wiley-VCH, Weinheim.
    • (1998) 12-proteins , pp. 237-251
    • Bothe, H.1    Buckel, W.2
  • 37
    • 0014027350 scopus 로고
    • Studies on the mechanism of action of cobalamide coenzymes. Chemical properties of the enzyme-coenzyme complex
    • Wagner, O.W., Lee, H.A., Jr., Frey, P.A. & Abeles, R.H. (1966). Studies on the mechanism of action of cobalamide coenzymes. Chemical properties of the enzyme-coenzyme complex. J. Biol. Chem. 241, 1751-1762.
    • (1966) J. Biol. Chem. , vol.241 , pp. 1751-1762
    • Wagner, O.W.1    Lee H.A., Jr.2    Frey, P.A.3    Abeles, R.H.4
  • 38
    • 0033119955 scopus 로고    scopus 로고
    • Crystallization and preliminary X-ray study of two crystal forms of Klebsiella oxytoca diol dehydratase-cyanocobalamin complex
    • Masuda, J., et al., Yasuoka, N. (1999). Crystallization and preliminary X-ray study of two crystal forms of Klebsiella oxytoca diol dehydratase-cyanocobalamin complex. Acta Crystallogr. D 55, 907-909.
    • (1999) Acta Crystallogr. D , vol.55 , pp. 907-909
    • Masuda, J.1    Yasuoka, N.2
  • 39
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project, No. 4 (1994). The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D 50, 760-763.
    • (1994) Acta Crystallogr. D , vol.50 , pp. 760-763
  • 40
    • 0031058188 scopus 로고    scopus 로고
    • Maximum likelihood heavy atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods
    • De la Fortelle, E. & Bricogne, G. (1997). Maximum likelihood heavy atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol., 276, 472-494.
    • (1997) Methods Enzymol. , vol.276 , pp. 472-494
    • De La Fortelle, E.1    Bricogne, G.2
  • 42
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov, G.N., Vagin, A.A. & Dodson, E.J. (1997). Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr, D 53, 240-255.
    • (1997) Acta Crystallogr, D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 43
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, J. (1991). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946
    • Kraulis, J.1
  • 44
    • 0028057108 scopus 로고
    • Raster3D version 2.0: A program for photorealistic molecular graphics
    • Merritt, E.A. & Murphy, M.E.P. (1994). Raster3D version 2.0: A program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869-873.
    • (1994) Acta Crystallogr. D , vol.50 , pp. 869-873
    • Merritt, E.A.1    Murphy, M.E.P.2
  • 45
    • 0030880598 scopus 로고    scopus 로고
    • SHELXL: High resolution refinement
    • Carter, C.W., Jr. & Sweet, R.M., eds, San Diego, Academic Press
    • Sheldrick, G.M. & Schneider, T.R. (1997). SHELXL: High resolution refinement. In Methods in Enzymology, 277, (Carter, C.W., Jr. & Sweet, R.M., eds), pp. 319-343, San Diego, Academic Press.
    • (1997) Methods in Enzymology , vol.277 , pp. 319-343
    • Sheldrick, G.M.1    Schneider, T.R.2
  • 46
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls, A., Sharp, K.A. & Honig, B. (1991). Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.