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Volumn 53, Issue 31, 2014, Pages 5150-5161

Kinetic and structural characterization of tunnel-perturbing mutants in Bradyrhizobium japonicum proline utilization A

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLATION;

EID: 84905980079     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi5007404     Document Type: Article
Times cited : (20)

References (46)
  • 1
    • 41149157883 scopus 로고    scopus 로고
    • Possible involvement of putA gene in Helicobacter pylori colonization in the stomach and motility
    • Nakajima, K., Inatsu, S., Mizote, T., Nagata, Y., Aoyama, K., Fukuda, Y., and Nagata, K. (2008) Possible involvement of putA gene in Helicobacter pylori colonization in the stomach and motility Biomed. Res. 29, 9-18
    • (2008) Biomed. Res. , vol.29 , pp. 9-18
    • Nakajima, K.1    Inatsu, S.2    Mizote, T.3    Nagata, Y.4    Aoyama, K.5    Fukuda, Y.6    Nagata, K.7
  • 2
    • 46449111827 scopus 로고    scopus 로고
    • Characterization of a Helicobacter hepaticus putA mutant strain in host colonization and oxidative stress
    • Krishnan, N., Doster, A. R., Duhamel, G. E., and Becker, D. F. (2008) Characterization of a Helicobacter hepaticus putA mutant strain in host colonization and oxidative stress Infect. Immun. 76, 3037-3044
    • (2008) Infect. Immun. , vol.76 , pp. 3037-3044
    • Krishnan, N.1    Doster, A.R.2    Duhamel, G.E.3    Becker, D.F.4
  • 4
    • 33745810581 scopus 로고    scopus 로고
    • Energy metabolism of trypanosomatids: Adaptation to available carbon sources
    • Bringaud, F., Riviere, L., and Coustou, V. (2006) Energy metabolism of trypanosomatids: Adaptation to available carbon sources Mol. Biochem. Parasitol. 149, 1-9
    • (2006) Mol. Biochem. Parasitol. , vol.149 , pp. 1-9
    • Bringaud, F.1    Riviere, L.2    Coustou, V.3
  • 5
    • 73449085767 scopus 로고    scopus 로고
    • Regulating alternative lifestyles in entomopathogenic bacteria
    • Crawford, J. M., Kontnik, R., and Clardy, J. (2010) Regulating alternative lifestyles in entomopathogenic bacteria Curr. Biol. 20, 69-74
    • (2010) Curr. Biol. , vol.20 , pp. 69-74
    • Crawford, J.M.1    Kontnik, R.2    Clardy, J.3
  • 6
    • 53849120906 scopus 로고    scopus 로고
    • PRODH variants and risk for schizophrenia
    • Willis, A., Bender, H. U., Steel, G., and Valle, D. (2008) PRODH variants and risk for schizophrenia Amino Acids 35, 673-679
    • (2008) Amino Acids , vol.35 , pp. 673-679
    • Willis, A.1    Bender, H.U.2    Steel, G.3    Valle, D.4
  • 7
    • 0037117578 scopus 로고    scopus 로고
    • A compelling genetic hypothesis for a complex disease: PRODH2/DGCR6 variation leads to schizophrenia susceptibility
    • Chakravarti, A. (2002) A compelling genetic hypothesis for a complex disease: PRODH2/DGCR6 variation leads to schizophrenia susceptibility Proc. Natl. Acad. Sci. U.S.A. 99, 4755-4756
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 4755-4756
    • Chakravarti, A.1
  • 8
    • 53849096017 scopus 로고    scopus 로고
    • The metabolism of proline, a stress substrate, modulates carcinogenic pathways
    • Phang, J. M., Donald, S. P., Pandhare, J., and Liu, Y. (2008) The metabolism of proline, a stress substrate, modulates carcinogenic pathways Amino Acids 35, 681-690
    • (2008) Amino Acids , vol.35 , pp. 681-690
    • Phang, J.M.1    Donald, S.P.2    Pandhare, J.3    Liu, Y.4
  • 9
    • 84893665746 scopus 로고    scopus 로고
    • PutA and proline metabolism
    • In (Hille, R. Miller, S. M. and Palfey, B. Eds.) pp, Walter de Gruyter, Boston.
    • Tanner, J. J. and Becker, D. F. (2013) PutA and proline metabolism. In Handbook of Flavoproteins (Hille, R., Miller, S. M., and Palfey, B., Eds.) pp 31-56, Walter de Gruyter, Boston.
    • (2013) Handbook of Flavoproteins , pp. 31-56
    • Tanner, J.J.1    Becker, D.F.2
  • 10
    • 0025895417 scopus 로고
    • Physiological significance of metabolic channelling
    • Ovadi, J. (1991) Physiological significance of metabolic channelling J. Theor. Biol. 152, 1-22
    • (1991) J. Theor. Biol. , vol.152 , pp. 1-22
    • Ovadi, J.1
  • 11
    • 0019631384 scopus 로고
    • A generalized theory of the transition time for sequential enzyme reactions
    • Easterby, J. S. (1981) A generalized theory of the transition time for sequential enzyme reactions Biochem. J. 199, 155-161
    • (1981) Biochem. J. , vol.199 , pp. 155-161
    • Easterby, J.S.1
  • 12
    • 0028898649 scopus 로고
    • Investigation of the mechanism of phosphoribosylamine transfer from glutamine phosphoribosylpyrophosphate amidotransferase to glycinamide ribonucleotide synthetase
    • Rudolph, J. and Stubbe, J. (1995) Investigation of the mechanism of phosphoribosylamine transfer from glutamine phosphoribosylpyrophosphate amidotransferase to glycinamide ribonucleotide synthetase Biochemistry 34, 2241-2250
    • (1995) Biochemistry , vol.34 , pp. 2241-2250
    • Rudolph, J.1    Stubbe, J.2
  • 13
    • 0034919604 scopus 로고    scopus 로고
    • Channeling of substrates and intermediates in enzyme-catalyzed reactions
    • Huang, X., Holden, H. M., and Raushel, F. M. (2001) Channeling of substrates and intermediates in enzyme-catalyzed reactions Annu. Rev. Biochem. 70, 149-180
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 149-180
    • Huang, X.1    Holden, H.M.2    Raushel, F.M.3
  • 14
    • 84857706529 scopus 로고    scopus 로고
    • Substrate channeling in proline metabolism
    • Arentson, B. W., Sanyal, N., and Becker, D. F. (2012) Substrate channeling in proline metabolism Front. Biosci. 17, 375-388
    • (2012) Front. Biosci. , vol.17 , pp. 375-388
    • Arentson, B.W.1    Sanyal, N.2    Becker, D.F.3
  • 15
    • 0032872139 scopus 로고    scopus 로고
    • Fundamental mechanisms of substrate channeling
    • Anderson, K. S. (1999) Fundamental mechanisms of substrate channeling Methods Enzymol. 308, 111-145
    • (1999) Methods Enzymol. , vol.308 , pp. 111-145
    • Anderson, K.S.1
  • 16
    • 0028980589 scopus 로고
    • Glutamate γ-semialdehyde as a natural transition state analogue inhibitor of Escherichia coli glucosamine-6-phosphate synthase
    • Bearne, S. L. and Wolfenden, R. (1995) Glutamate γ-semialdehyde as a natural transition state analogue inhibitor of Escherichia coli glucosamine-6-phosphate synthase Biochemistry 34, 11515-11520
    • (1995) Biochemistry , vol.34 , pp. 11515-11520
    • Bearne, S.L.1    Wolfenden, R.2
  • 17
    • 0035874473 scopus 로고    scopus 로고
    • Inhibition of Escherichia coli CTP synthase by glutamate γ-semialdehyde and the role of the allosteric effector GTP in glutamine hydrolysis
    • Bearne, S. L., Hekmat, O., and Macdonnell, J. E. (2001) Inhibition of Escherichia coli CTP synthase by glutamate γ-semialdehyde and the role of the allosteric effector GTP in glutamine hydrolysis Biochem. J. 356, 223-232
    • (2001) Biochem. J. , vol.356 , pp. 223-232
    • Bearne, S.L.1    Hekmat, O.2    Macdonnell, J.E.3
  • 18
    • 0033534173 scopus 로고    scopus 로고
    • The small subunit of carbamoyl phosphate synthetase: Snapshots along the reaction pathway
    • Thoden, J. B., Huang, X., Raushel, F. M., and Holden, H. M. (1999) The small subunit of carbamoyl phosphate synthetase: Snapshots along the reaction pathway Biochemistry 38, 16158-16166
    • (1999) Biochemistry , vol.38 , pp. 16158-16166
    • Thoden, J.B.1    Huang, X.2    Raushel, F.M.3    Holden, H.M.4
  • 19
    • 0035805636 scopus 로고    scopus 로고
    • Pyridoxal phosphate de-activation by pyrroline-5-carboxylic acid. Increased risk of vitamin B6 deficiency and seizures in hyperprolinemia type II
    • Farrant, R. D., Walker, V., Mills, G. A., Mellor, J. M., and Langley, G. J. (2001) Pyridoxal phosphate de-activation by pyrroline-5-carboxylic acid. Increased risk of vitamin B6 deficiency and seizures in hyperprolinemia type II J. Biol. Chem. 276, 15107-15116
    • (2001) J. Biol. Chem. , vol.276 , pp. 15107-15116
    • Farrant, R.D.1    Walker, V.2    Mills, G.A.3    Mellor, J.M.4    Langley, G.J.5
  • 20
    • 0032526547 scopus 로고    scopus 로고
    • The PutA protein of Salmonella typhimurium catalyzes the two steps of proline degradation via a leaky channel
    • Surber, M. W. and Maloy, S. (1998) The PutA protein of Salmonella typhimurium catalyzes the two steps of proline degradation via a leaky channel Arch. Biochem. Biophys. 354, 281-287
    • (1998) Arch. Biochem. Biophys. , vol.354 , pp. 281-287
    • Surber, M.W.1    Maloy, S.2
  • 22
    • 84895795810 scopus 로고    scopus 로고
    • Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone binding site
    • Singh, H., Arentson, B. W., Becker, D. F., and Tanner, J. J. (2014) Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone binding site Proc. Natl. Acad. Sci. U.S.A. 111, 3389-3394
    • (2014) Proc. Natl. Acad. Sci. U.S.A. , vol.111 , pp. 3389-3394
    • Singh, H.1    Arentson, B.W.2    Becker, D.F.3    Tanner, J.J.4
  • 23
    • 84893659587 scopus 로고    scopus 로고
    • Evidence for hysteretic substrate channeling in the proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase coupled reaction of proline utilization A (PutA)
    • Moxley, M. A., Sanyal, N., Krishnan, N., Tanner, J. J., and Becker, D. F. (2014) Evidence for hysteretic substrate channeling in the proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase coupled reaction of proline utilization A (PutA) J. Biol. Chem. 289, 3639-3651
    • (2014) J. Biol. Chem. , vol.289 , pp. 3639-3651
    • Moxley, M.A.1    Sanyal, N.2    Krishnan, N.3    Tanner, J.J.4    Becker, D.F.5
  • 24
    • 0016654521 scopus 로고
    • Improved chemical synthesis and enzymatic assay of Δ1-pyrroline-5- carboxylic acid
    • Williams, I. and Frank, L. (1975) Improved chemical synthesis and enzymatic assay of Δ1-pyrroline-5-carboxylic acid Anal. Biochem. 64, 85-97
    • (1975) Anal. Biochem. , vol.64 , pp. 85-97
    • Williams, I.1    Frank, L.2
  • 25
    • 84856946727 scopus 로고    scopus 로고
    • Rapid reaction kinetics of proline dehydrogenase in the multifunctional proline utilization A protein
    • Moxley, M. A. and Becker, D. F. (2012) Rapid reaction kinetics of proline dehydrogenase in the multifunctional proline utilization A protein Biochemistry 51, 511-520
    • (2012) Biochemistry , vol.51 , pp. 511-520
    • Moxley, M.A.1    Becker, D.F.2
  • 26
    • 21744454349 scopus 로고    scopus 로고
    • Characterization of a bifunctional PutA homologue from Bradyrhizobium japonicum and identification of an active site residue that modulates proline reduction of the flavin adenine dinucleotide cofactor
    • Krishnan, N. and Becker, D. F. (2005) Characterization of a bifunctional PutA homologue from Bradyrhizobium japonicum and identification of an active site residue that modulates proline reduction of the flavin adenine dinucleotide cofactor Biochemistry 44, 9130-9139
    • (2005) Biochemistry , vol.44 , pp. 9130-9139
    • Krishnan, N.1    Becker, D.F.2
  • 27
    • 81755173365 scopus 로고    scopus 로고
    • Steady-state kinetic mechanism of the proline:ubiquinone oxidoreductase activity of proline utilization A (PutA) from Escherichia coli
    • Moxley, M. A., Tanner, J. J., and Becker, D. F. (2011) Steady-state kinetic mechanism of the proline:ubiquinone oxidoreductase activity of proline utilization A (PutA) from Escherichia coli Arch. Biochem. Biophys. 516, 113-120
    • (2011) Arch. Biochem. Biophys. , vol.516 , pp. 113-120
    • Moxley, M.A.1    Tanner, J.J.2    Becker, D.F.3
  • 28
    • 0034669323 scopus 로고    scopus 로고
    • The use of protocatechuate dioxygenase for maintaining anaerobic conditions in biochemical experiments
    • Patil, P. V. and Ballou, D. P. (2000) The use of protocatechuate dioxygenase for maintaining anaerobic conditions in biochemical experiments Anal. Biochem. 286, 187-192
    • (2000) Anal. Biochem. , vol.286 , pp. 187-192
    • Patil, P.V.1    Ballou, D.P.2
  • 29
    • 53749084542 scopus 로고    scopus 로고
    • Three crystal forms of the bifunctional enzyme proline utilization A (PutA) from Bradyrhizobium japonicum
    • Schuermann, J. P., White, T. A., Srivastava, D., Karr, D. B., and Tanner, J. J. (2008) Three crystal forms of the bifunctional enzyme proline utilization A (PutA) from Bradyrhizobium japonicum Acta Crystallogr. F64, 949-953
    • (2008) Acta Crystallogr. , vol.64 , pp. 949-953
    • Schuermann, J.P.1    White, T.A.2    Srivastava, D.3    Karr, D.B.4    Tanner, J.J.5
  • 30
    • 33644874235 scopus 로고    scopus 로고
    • The integration of macromolecular diffraction data
    • Leslie, A. G. (2006) The integration of macromolecular diffraction data Acta Crystallogr. D62, 48-57
    • (2006) Acta Crystallogr. , vol.62 , pp. 48-57
    • Leslie, A.G.1
  • 31
    • 33644875355 scopus 로고    scopus 로고
    • Scaling and assessment of data quality
    • Evans, P. (2006) Scaling and assessment of data quality Acta Crystallogr. D62, 72-82
    • (2006) Acta Crystallogr. , vol.62 , pp. 72-82
    • Evans, P.1
  • 36
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of cavities in macromolecular structures
    • Kleywegt, G. J. and Jones, T. A. (1994) Detection, delineation, measurement and display of cavities in macromolecular structures Acta Crystallogr. D50, 178-185
    • (1994) Acta Crystallogr. , vol.50 , pp. 178-185
    • Kleywegt, G.J.1    Jones, T.A.2
  • 38
    • 35748972048 scopus 로고    scopus 로고
    • MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels
    • Petrek, M., Kosinova, P., Koca, J., and Otyepka, M. (2007) MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels Structure 15, 1357-1363
    • (2007) Structure , vol.15 , pp. 1357-1363
    • Petrek, M.1    Kosinova, P.2    Koca, J.3    Otyepka, M.4
  • 41
    • 79955574923 scopus 로고    scopus 로고
    • version 1.3r1 () Schrodinger, LLC, Portland, OR.
    • The PyMOL Molecular Graphics System, version 1.3r1 (2010) Schrodinger, LLC, Portland, OR.
    • (2010) The PyMOL Molecular Graphics System
  • 42
    • 0029585981 scopus 로고
    • Kinetic characterization of channel impaired mutants of tryptophan synthase
    • Anderson, K. S., Kim, A. Y., Quillen, J. M., Sayers, E., Yang, X. J., and Miles, E. W. (1995) Kinetic characterization of channel impaired mutants of tryptophan synthase J. Biol. Chem. 270, 29936-29944
    • (1995) J. Biol. Chem. , vol.270 , pp. 29936-29944
    • Anderson, K.S.1    Kim, A.Y.2    Quillen, J.M.3    Sayers, E.4    Yang, X.J.5    Miles, E.W.6
  • 43
    • 84861686181 scopus 로고    scopus 로고
    • Biochemical and structural characterization of the Arabidopsis bifunctional enzyme dethiobiotin synthetase-diaminopelargonic acid aminotransferase: Evidence for substrate channeling in biotin synthesis
    • Cobessi, D., Dumas, R., Pautre, V., Meinguet, C., Ferrer, J. L., and Alban, C. (2012) Biochemical and structural characterization of the Arabidopsis bifunctional enzyme dethiobiotin synthetase-diaminopelargonic acid aminotransferase: Evidence for substrate channeling in biotin synthesis Plant Cell 24, 1608-1625
    • (2012) Plant Cell , vol.24 , pp. 1608-1625
    • Cobessi, D.1    Dumas, R.2    Pautre, V.3    Meinguet, C.4    Ferrer, J.L.5    Alban, C.6
  • 44
    • 0025006579 scopus 로고
    • The tryptophan synthase bienzyme complex transfers indole between the α- And β-sites via a 25-30 Å long tunnel
    • Dunn, M. F., Aguilar, V., Brzovic, P., Drewe, W. F., Jr., Houben, K. F., Leja, C. A., and Roy, M. (1990) The tryptophan synthase bienzyme complex transfers indole between the α- and β-sites via a 25-30 Å long tunnel Biochemistry 29, 8598-8607
    • (1990) Biochemistry , vol.29 , pp. 8598-8607
    • Dunn, M.F.1    Aguilar, V.2    Brzovic, P.3    Drewe Jr., W.F.4    Houben, K.F.5    Leja, C.A.6    Roy, M.7
  • 45
    • 0027419533 scopus 로고
    • Conformational change and membrane association of the PutA protein are coincident with reduction of its FAD cofactor by proline
    • Brown, E. D. and Wood, J. M. (1993) Conformational change and membrane association of the PutA protein are coincident with reduction of its FAD cofactor by proline J. Biol. Chem. 268, 8972-8979
    • (1993) J. Biol. Chem. , vol.268 , pp. 8972-8979
    • Brown, E.D.1    Wood, J.M.2


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