메뉴 건너뛰기




Volumn 391, Issue 3, 2009, Pages 609-620

Crystal Structure and Putative Mechanism of 3-Methylitaconate-Δ-isomerase from Eubacterium barkeri

Author keywords

DapF family fold; methylitaconate isomerase; open and closed conformations; PrpF protein; X ray structure

Indexed keywords

3 METHYLITACONATE DELTA ISOMERASE; BACTERIAL ENZYME; CYSTEINE; GLUTAMIC ACID; HISTIDINE; ISOMERASE; ISOPENTENYL DIPHOSPHATE DELTA ISOMERASE; LYSINE; SERINE; UNCLASSIFIED DRUG;

EID: 67651149462     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.06.052     Document Type: Article
Times cited : (12)

References (43)
  • 2
    • 0017343370 scopus 로고
    • Energy conservation in chemotropic anaerobic bacteria
    • Thauer R.K., Jungermann K., and Decker K. Energy conservation in chemotropic anaerobic bacteria. Bacteriol. Rev. 41 (1977) 100-180
    • (1977) Bacteriol. Rev. , vol.41 , pp. 100-180
    • Thauer, R.K.1    Jungermann, K.2    Decker, K.3
  • 4
    • 50149089407 scopus 로고    scopus 로고
    • Structural and kinetic properties of a β-hydroxyacid dehydrogenase involved in nicotinate fermentation
    • Reitz S., Alhapel A., Essen L.-O., and Pierik A.J. Structural and kinetic properties of a β-hydroxyacid dehydrogenase involved in nicotinate fermentation. J. Mol. Biol. 382 (2008) 802-811
    • (2008) J. Mol. Biol. , vol.382 , pp. 802-811
    • Reitz, S.1    Alhapel, A.2    Essen, L.-O.3    Pierik, A.J.4
  • 5
    • 56249083874 scopus 로고    scopus 로고
    • The crystal structure of enamidase: a bifunctional enzyme of nicotinate catabolism
    • Kress D., Alhapel A., Pierik A.J., and Essen L.-O. The crystal structure of enamidase: a bifunctional enzyme of nicotinate catabolism. J. Mol. Biol. 384 (2008) 837-847
    • (2008) J. Mol. Biol. , vol.384 , pp. 837-847
    • Kress, D.1    Alhapel, A.2    Pierik, A.J.3    Essen, L.-O.4
  • 6
    • 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 (1994) 101-109
    • (1994) Eur. J. Biochem. , vol.221 , pp. 101-109
    • Beatrix, B.1    Zelder, O.2    Linder, D.3    Buckel, W.4
  • 7
    • 0015239539 scopus 로고
    • 12-dependent) and methylitaconate isomerase
    • 12-dependent) and methylitaconate isomerase. J. Biol. Chem. 246 (1971) 3378-3388
    • (1971) J. Biol. Chem. , vol.246 , pp. 3378-3388
    • Kung, H.-F.1    Stadtman, T.C.2
  • 8
    • 0023049434 scopus 로고
    • On the steric course of adenosylcobalamin-dependent 2-methyleneglutarate mutase reaction in Clostridium barkeri
    • Hartrampf G., and Buckel W. On the steric course of adenosylcobalamin-dependent 2-methyleneglutarate mutase reaction in Clostridium barkeri. Eur. J. Biochem. 156 (1986) 301-304
    • (1986) Eur. J. Biochem. , vol.156 , pp. 301-304
    • Hartrampf, G.1    Buckel, W.2
  • 9
    • 0024457799 scopus 로고
    • Assay and purification of the adenosylcobalamin-dependent 2-methyleneglutarate mutase from Clostridium barkeri
    • Michel C., Hartrampf G., and Buckel W. Assay and purification of the adenosylcobalamin-dependent 2-methyleneglutarate mutase from Clostridium barkeri. Eur. J. Biochem. 184 (1989) 103-107
    • (1989) Eur. J. Biochem. , vol.184 , pp. 103-107
    • Michel, C.1    Hartrampf, G.2    Buckel, W.3
  • 10
    • 67651181166 scopus 로고
    • Diploma Thesis, Philipps-Universität, Marburg, Germany
    • Bröker, G. (1995.) Diploma Thesis, Philipps-Universität, Marburg, Germany
    • (1995)
    • Bröker, G.1
  • 11
    • 34547609909 scopus 로고    scopus 로고
    • The non-mevalonate pathway of isoprenoid precursor biosynthesis
    • Hunter W.N. The non-mevalonate pathway of isoprenoid precursor biosynthesis. J. Biol. Chem. 282 (2007) 21573-21577
    • (2007) J. Biol. Chem. , vol.282 , pp. 21573-21577
    • Hunter, W.N.1
  • 12
    • 0015215170 scopus 로고
    • Purification and kinetic properties of aconitate isomerase from Pseudomonas putida
    • Klinman J.P., and Rose I.A. Purification and kinetic properties of aconitate isomerase from Pseudomonas putida. Biochemistry 10 (1971) 2253-2259
    • (1971) Biochemistry , vol.10 , pp. 2253-2259
    • Klinman, J.P.1    Rose, I.A.2
  • 13
    • 0029839587 scopus 로고    scopus 로고
    • Fermentation of trans-aconitate via citrate, oxaloacetate and pyruvate by Acidaminococcus fermentans
    • Härtel U., and Buckel W. Fermentation of trans-aconitate via citrate, oxaloacetate and pyruvate by Acidaminococcus fermentans. Arch. Microbiol. 166 (1996) 342-349
    • (1996) Arch. Microbiol. , vol.166 , pp. 342-349
    • Härtel, U.1    Buckel, W.2
  • 14
    • 0005226507 scopus 로고
    • Biosynthesis of terpenes. VII. Isopentenyl pyrophosphate isomerase
    • Agranoff B.W., Eggerer H., Henning U., and Lynen F. Biosynthesis of terpenes. VII. Isopentenyl pyrophosphate isomerase. J. Biol. Chem. 235 (1960) 326-332
    • (1960) J. Biol. Chem. , vol.235 , pp. 326-332
    • Agranoff, B.W.1    Eggerer, H.2    Henning, U.3    Lynen, F.4
  • 15
    • 0028325819 scopus 로고
    • Identification of Cys139 and Glu207 as catalytically important groups in the active site of isopentenyl diphosphate:dimethylallyl diphosphate isomerase
    • Street I.P., Coffman H.R., Baker J.A., and Poulter C.D. Identification of Cys139 and Glu207 as catalytically important groups in the active site of isopentenyl diphosphate:dimethylallyl diphosphate isomerase. Biochemistry 33 (1994) 4212-4217
    • (1994) Biochemistry , vol.33 , pp. 4212-4217
    • Street, I.P.1    Coffman, H.R.2    Baker, J.A.3    Poulter, C.D.4
  • 16
    • 33748360507 scopus 로고    scopus 로고
    • Escherichia coli type I isopentenyl diphosphate isomerase: structural and catalytic roles for divalent metals
    • Lee S., and Poulter C.D. Escherichia coli type I isopentenyl diphosphate isomerase: structural and catalytic roles for divalent metals. J. Am. Chem. Soc. 128 (2006) 11545-11550
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 11545-11550
    • Lee, S.1    Poulter, C.D.2
  • 17
    • 66149104732 scopus 로고    scopus 로고
    • New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase
    • Unno H., Yamashita S., Ikeda Y., Sekiguchi S.Y., Yoshida N., Yoshimura T., et al. New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase. J. Biol. Chem. 284 (2009) 9160-9167
    • (2009) J. Biol. Chem. , vol.284 , pp. 9160-9167
    • Unno, H.1    Yamashita, S.2    Ikeda, Y.3    Sekiguchi, S.Y.4    Yoshida, N.5    Yoshimura, T.6
  • 18
    • 34250766201 scopus 로고    scopus 로고
    • The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins
    • Schmidt T.G., and Skerra A. The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins. Nat. Protoc. 2 (2007) 1528-1535
    • (2007) Nat. Protoc. , vol.2 , pp. 1528-1535
    • Schmidt, T.G.1    Skerra, A.2
  • 19
    • 34250859670 scopus 로고    scopus 로고
    • The three-dimensional crystal structure of the PrpF protein from Shewanella oneidensis complexed with trans-aconitate: insights into its biological function
    • Garvey G.S., Rocco C.J., Escalante-Semerena J.C., and Rayment I. The three-dimensional crystal structure of the PrpF protein from Shewanella oneidensis complexed with trans-aconitate: insights into its biological function. Protein Sci. 16 (2007) 1274-1284
    • (2007) Protein Sci. , vol.16 , pp. 1274-1284
    • Garvey, G.S.1    Rocco, C.J.2    Escalante-Semerena, J.C.3    Rayment, I.4
  • 20
    • 0032564314 scopus 로고    scopus 로고
    • Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase
    • Cirilli M., Zheng R., Scapin G., and Blanchard J.S. Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase. Biochemistry 37 (1998) 16452-16458
    • (1998) Biochemistry , vol.37 , pp. 16452-16458
    • Cirilli, M.1    Zheng, R.2    Scapin, G.3    Blanchard, J.S.4
  • 22
    • 32444448479 scopus 로고    scopus 로고
    • Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase
    • Buschiazzo A., Goytia M., Schaeffer F., Degrave W., Shepard W., Gregoire C., et al. Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase. Proc. Natl Acad. Sci. USA 103 (2006) 1705-1710
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 1705-1710
    • Buschiazzo, A.1    Goytia, M.2    Schaeffer, F.3    Degrave, W.4    Shepard, W.5    Gregoire, C.6
  • 23
  • 24
    • 0002580781 scopus 로고    scopus 로고
    • Simplified error estimation a la Cruickshank in macromolecular crystallography
    • Murshudov G.N., and Dodson E.J. Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newslett. Protein Crystallogr. 33 (1997) 31-39
    • (1997) CCP4 Newslett. Protein Crystallogr. , vol.33 , pp. 31-39
    • Murshudov, G.N.1    Dodson, E.J.2
  • 25
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Krissinel E., and Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 (2004) 2256-2268
    • (2004) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 27
    • 0030221366 scopus 로고    scopus 로고
    • Human isopentenyl diphosphate:dimethylallyl diphosphate isomerase: overproduction, purification, and characterization
    • Hahn F.M., Xuan J.W., Chambers A.F., and Poulter C.D. Human isopentenyl diphosphate:dimethylallyl diphosphate isomerase: overproduction, purification, and characterization. Arch. Biochem. Biophys. 332 (1996) 30-34
    • (1996) Arch. Biochem. Biophys. , vol.332 , pp. 30-34
    • Hahn, F.M.1    Xuan, J.W.2    Chambers, A.F.3    Poulter, C.D.4
  • 28
    • 0034095188 scopus 로고    scopus 로고
    • Methylcitrate synthase from Aspergillus nidulans: implications for propionate as an antifungal agent
    • Brock M., Fischer R., Lindner D., and Buckel W. Methylcitrate synthase from Aspergillus nidulans: implications for propionate as an antifungal agent. Mol. Microbiol. 35 (2000) 961-973
    • (2000) Mol. Microbiol. , vol.35 , pp. 961-973
    • Brock, M.1    Fischer, R.2    Lindner, D.3    Buckel, W.4
  • 29
    • 0030714624 scopus 로고    scopus 로고
    • Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria
    • Textor S., Wendisch V.F., DeGraaf A.A., Müller U., Lindner M.I., and Buckel W. Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria. Arch. Microbiol. 168 (1997) 428-436
    • (1997) Arch. Microbiol. , vol.168 , pp. 428-436
    • Textor, S.1    Wendisch, V.F.2    DeGraaf, A.A.3    Müller, U.4    Lindner, M.I.5    Buckel, W.6
  • 30
    • 0036449408 scopus 로고    scopus 로고
    • Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase
    • Brock M., Maerker C., Schutz A., Völker U., and Buckel W. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur. J. Biochem. 269 (2002) 6184-6194
    • (2002) Eur. J. Biochem. , vol.269 , pp. 6184-6194
    • Brock, M.1    Maerker, C.2    Schutz, A.3    Völker, U.4    Buckel, W.5
  • 31
    • 0035901535 scopus 로고    scopus 로고
    • In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate
    • Horswill A.R., and Escalante-Semerena J.C. In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate. Biochemistry 40 (2001) 4703-4713
    • (2001) Biochemistry , vol.40 , pp. 4703-4713
    • Horswill, A.R.1    Escalante-Semerena, J.C.2
  • 32
    • 0016699732 scopus 로고
    • Substrate stereochemistry of the enoyl-CoA hydratase reaction
    • Willadsen P., and Eggerer H. Substrate stereochemistry of the enoyl-CoA hydratase reaction. Eur. J. Biochem. 54 (1975) 247-252
    • (1975) Eur. J. Biochem. , vol.54 , pp. 247-252
    • Willadsen, P.1    Eggerer, H.2
  • 35
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Carter C.W., and Sweet R.M. (Eds), Academic Press, New York, NY
    • Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. In: Carter C.W., and Sweet R.M. (Eds). Methods in Enzymology, Macromolecular Crystallography, Part A vol. 276 (1997), Academic Press, New York, NY 307-326
    • (1997) Methods in Enzymology, Macromolecular Crystallography, Part A , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 36
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: an automated program for molecular replacement
    • Vagin A., and Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30 (1997) 1022-1025
    • (1997) J. Appl. Crystallogr. , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 39
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R.A., McArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    McArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 41
    • 0025912338 scopus 로고
    • Molecular recognition: conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors
    • Hubbard S.J., Campbell S.F., and Thornton J.M. Molecular recognition: conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J. Mol. Biol. 220 (1991) 507-530
    • (1991) J. Mol. Biol. , vol.220 , pp. 507-530
    • Hubbard, S.J.1    Campbell, S.F.2    Thornton, J.M.3
  • 43
    • 0027412196 scopus 로고
    • ALSCRIPT: a tool to format multiple sequence alignments
    • Barton G.J. ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 6 (1993) 37-40
    • (1993) Protein Eng. , vol.6 , pp. 37-40
    • Barton, G.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.