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Volumn 373, Issue 4, 2007, Pages 866-876

Structure and Mechanism of HpcH: A Metal Ion Dependent Class II Aldolase from the Homoprotocatechuate Degradation Pathway of Escherichia coli

Author keywords

aromatic degradation; Catalytic Mechanism; Crystal Structure; homoprotocatechuate; ldolase

Indexed keywords

2 DEHYDRO 3 DEOXYGALACTARATE ALDOLASE; 3,4 DIHYDROXYPHENYLACETIC ACID; 4 HYDROXY 2 OXO HEPTANE 1,7 DIOATE ALDOLASE; ARGININE; ESCHERICHIA COLI PROTEIN; FRUCTOSE BISPHOSPHATE ALDOLASE; HISTIDINE; MAGNESIUM; METAL ION; OXAMIC ACID; UNCLASSIFIED DRUG;

EID: 34848891771     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.06.048     Document Type: Article
Times cited : (26)

References (42)
  • 1
    • 16544381551 scopus 로고    scopus 로고
    • Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility
    • Diaz E. Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int. Microbiol. 7 (2004) 173-180
    • (2004) Int. Microbiol. , vol.7 , pp. 173-180
    • Diaz, E.1
  • 3
    • 16344371832 scopus 로고    scopus 로고
    • Dual substrate biodegradation of a non-ionic surfactant and pentachlorophenol by Sphingomonas chlorophenolica RA2
    • Bielefeldt A.R., and Cort T. Dual substrate biodegradation of a non-ionic surfactant and pentachlorophenol by Sphingomonas chlorophenolica RA2. Biotechnol. Bioeng. 89 (2005) 680-689
    • (2005) Biotechnol. Bioeng. , vol.89 , pp. 680-689
    • Bielefeldt, A.R.1    Cort, T.2
  • 4
    • 0019303264 scopus 로고
    • Catabolism of 3- and 4- hydroxyphenylacetate by the 3,4-dihydroxyphenylacetate pathway in Escherichia coli
    • Cooper R.A., and Skinner M.A. Catabolism of 3- and 4- hydroxyphenylacetate by the 3,4-dihydroxyphenylacetate pathway in Escherichia coli. J. Bacteriol. 143 (1980) 302-306
    • (1980) J. Bacteriol. , vol.143 , pp. 302-306
    • Cooper, R.A.1    Skinner, M.A.2
  • 5
    • 0028958247 scopus 로고
    • Sequence of the hpcC and hpcG genes of the meta-fission homoprotocatechuic acid pathway of Escherichia coli C: nearly 40% amino-acid identity with the analogous enzymes of the catechol pathway
    • Roper D.I., Stringfellow J.M., and Cooper R.A. Sequence of the hpcC and hpcG genes of the meta-fission homoprotocatechuic acid pathway of Escherichia coli C: nearly 40% amino-acid identity with the analogous enzymes of the catechol pathway. Gene 156 (1995) 47-51
    • (1995) Gene , vol.156 , pp. 47-51
    • Roper, D.I.1    Stringfellow, J.M.2    Cooper, R.A.3
  • 6
    • 0024110374 scopus 로고
    • Molecular cloning, expression, and analysis of the genes of the homoprotocatechuate catabolic pathway of Escherichia coli C
    • Jenkins J.R., and Cooper R.A. Molecular cloning, expression, and analysis of the genes of the homoprotocatechuate catabolic pathway of Escherichia coli C. J. Bacteriol. 170 (1988) 5317-5324
    • (1988) J. Bacteriol. , vol.170 , pp. 5317-5324
    • Jenkins, J.R.1    Cooper, R.A.2
  • 7
    • 0027410220 scopus 로고
    • The Escherichia coli C homoprotocatechuate degradative operon: hpc gene order, direction of transcription and control of expression
    • Roper D.I., Fawcett T., and Cooper R.A. The Escherichia coli C homoprotocatechuate degradative operon: hpc gene order, direction of transcription and control of expression. Mol. Gen. Genet. 237 (1993) 241-250
    • (1993) Mol. Gen. Genet. , vol.237 , pp. 241-250
    • Roper, D.I.1    Fawcett, T.2    Cooper, R.A.3
  • 8
    • 0030029182 scopus 로고    scopus 로고
    • Molecular characterization of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli W: engineering a mobile aromatic degradative cluster
    • Prieto M.A., Diaz E., and Garcia J.L. Molecular characterization of the 4-hydroxyphenylacetate catabolic pathway of Escherichia coli W: engineering a mobile aromatic degradative cluster. J. Bacteriol. 178 (1996) 111-120
    • (1996) J. Bacteriol. , vol.178 , pp. 111-120
    • Prieto, M.A.1    Diaz, E.2    Garcia, J.L.3
  • 9
    • 0030060180 scopus 로고    scopus 로고
    • Enzymatic ketonization of 2- hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases
    • Subramanya H.S., Roper D.I., Dauter Z., Dodson E.J., Davies G.J., Wilson K.S., and Wigley D.B. Enzymatic ketonization of 2- hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases. Biochemistry 35 (1996) 792-802
    • (1996) Biochemistry , vol.35 , pp. 792-802
    • Subramanya, H.S.1    Roper, D.I.2    Dauter, Z.3    Dodson, E.J.4    Davies, G.J.5    Wilson, K.S.6    Wigley, D.B.7
  • 10
    • 0037022802 scopus 로고    scopus 로고
    • The crystal structure of HpcE, a bifunctional decarboxylase/isomerase with a multifunctional fold
    • Tame J.R.H., Namba K., Dodson E.J., and Roper D.I. The crystal structure of HpcE, a bifunctional decarboxylase/isomerase with a multifunctional fold. Biochemistry 41 (2002) 2982-2989
    • (2002) Biochemistry , vol.41 , pp. 2982-2989
    • Tame, J.R.H.1    Namba, K.2    Dodson, E.J.3    Roper, D.I.4
  • 11
    • 1642264726 scopus 로고    scopus 로고
    • Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases
    • Vetting M.W., Wackett L.P., Que Jr. L., Lipscomb J.D., and Ohlendorf D.H. Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases. J. Bacteriol. 186 (2004) 1945-1958
    • (2004) J. Bacteriol. , vol.186 , pp. 1945-1958
    • Vetting, M.W.1    Wackett, L.P.2    Que Jr., L.3    Lipscomb, J.D.4    Ohlendorf, D.H.5
  • 12
    • 0032511427 scopus 로고    scopus 로고
    • Stereochemical and isotopic labeling studies of 2-oxo-hept-4-ene-1,7-dioate hydratase: evidence for an enzyme-catalyzed ketonization step in the hydration reaction
    • Burks E.A., Johnson Jr. W.H., and Whitman C.P. Stereochemical and isotopic labeling studies of 2-oxo-hept-4-ene-1,7-dioate hydratase: evidence for an enzyme-catalyzed ketonization step in the hydration reaction. J. Am. Chem. Soc. 120 (1998) 7665-7675
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 7665-7675
    • Burks, E.A.1    Johnson Jr., W.H.2    Whitman, C.P.3
  • 13
    • 0032518288 scopus 로고    scopus 로고
    • Purification, characterisation and reaction mechanism of monofunctional 2-hydroxypentadienoic acid hydratase from Escherichia coli
    • Pollard J.R., and Bugg T.D. Purification, characterisation and reaction mechanism of monofunctional 2-hydroxypentadienoic acid hydratase from Escherichia coli. Eur. J. Biochem. 251 (1998) 98-106
    • (1998) Eur. J. Biochem. , vol.251 , pp. 98-106
    • Pollard, J.R.1    Bugg, T.D.2
  • 14
    • 0034254465 scopus 로고    scopus 로고
    • Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism
    • Izard T., and Blackwell N.C. Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism. EMBO J. 19 (2000) 3849-3856
    • (2000) EMBO J. , vol.19 , pp. 3849-3856
    • Izard, T.1    Blackwell, N.C.2
  • 15
    • 21844459727 scopus 로고    scopus 로고
    • Purification and biochemical characterization of a pyruvate-specific class II aldolase, HpaI
    • Wang W., and Seah S.Y. Purification and biochemical characterization of a pyruvate-specific class II aldolase, HpaI. Biochemistry 44 (2005) 9227-9255
    • (2005) Biochemistry , vol.44 , pp. 9227-9255
    • Wang, W.1    Seah, S.Y.2
  • 16
    • 0031665192 scopus 로고    scopus 로고
    • Substrate selectivity and biochemical properties of 4-hydroxy-2-keto-pentanoic acid aldolase from Escherichia coli
    • Pollard J.R., Rialland D., and Bugg T.D. Substrate selectivity and biochemical properties of 4-hydroxy-2-keto-pentanoic acid aldolase from Escherichia coli. Appl. Environ. Microbiol. 64 (1998) 4093-4094
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 4093-4094
    • Pollard, J.R.1    Rialland, D.2    Bugg, T.D.3
  • 17
    • 0029559910 scopus 로고
    • Gene cloning, purification, and characterization of thermostable and halophilic leucine dehydrogenase from a halophilic thermophile, Bacillus licheniformis TSN9
    • Nagata S., Bakthavatsalam S., Galkin A.G., Asada H., Sakai S., Esaki N., et al. Gene cloning, purification, and characterization of thermostable and halophilic leucine dehydrogenase from a halophilic thermophile, Bacillus licheniformis TSN9. Appl. Environ. Microbiol. 44 (1995) 432-438
    • (1995) Appl. Environ. Microbiol. , vol.44 , pp. 432-438
    • Nagata, S.1    Bakthavatsalam, S.2    Galkin, A.G.3    Asada, H.4    Sakai, S.5    Esaki, N.6
  • 18
    • 0037453002 scopus 로고    scopus 로고
    • Modifying the stereochemistry of an enzyme-catalyzed reaction by directed evolution
    • Williams G., J., Domann S., Nelson A., and Berry A. Modifying the stereochemistry of an enzyme-catalyzed reaction by directed evolution. Proc. Natl Acad. Sci. USA 100 (2003) 3143-3148
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 3143-3148
    • Williams, G.1    Domann, S.2    Nelson, A.3    Berry, A.4
  • 19
    • 18044366809 scopus 로고    scopus 로고
    • A thermostable variant of fructose bisphosphate aldolase constructed by directed evolution also shows increased stability in organic solvents
    • Hao J., and Berry A. A thermostable variant of fructose bisphosphate aldolase constructed by directed evolution also shows increased stability in organic solvents. Protein Eng. Des. Sel. 17 (2004) 689-697
    • (2004) Protein Eng. Des. Sel. , vol.17 , pp. 689-697
    • Hao, J.1    Berry, A.2
  • 20
    • 0028103275 scopus 로고
    • The CCP4 suite: programs for protein crystallography
    • CCP4
    • CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
    • (1994) Acta Crystallog. sect. D , vol.50 , pp. 760-763
  • 21
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L., and Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233 (1993) 123-138
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 22
    • 0028871926 scopus 로고
    • Dali: a network tool for protein structure comparison
    • Holm L., and Sander C. Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20 (1995) 478-480
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 478-480
    • Holm, L.1    Sander, C.2
  • 23
    • 0032485628 scopus 로고    scopus 로고
    • +)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 Å resolution: ATP binding over a barrel
    • +)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 Å resolution: ATP binding over a barrel. Biochemistry 37 (1998) 6247-6255
    • (1998) Biochemistry , vol.37 , pp. 6247-6255
    • Larsen, T.M.1    Benning, M.M.2    Rayment, I.3    Reed, G.H.4
  • 24
    • 33751570904 scopus 로고    scopus 로고
    • The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function
    • Goulding C.W., Bowers P.M., Segelke B., Lekin T., Kim C.Y., Terwilliger T.C., and Eisenberg D. The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function. J. Mol. Biol. 365 (2007) 275-283
    • (2007) J. Mol. Biol. , vol.365 , pp. 275-283
    • Goulding, C.W.1    Bowers, P.M.2    Segelke, B.3    Lekin, T.4    Kim, C.Y.5    Terwilliger, T.C.6    Eisenberg, D.7
  • 25
    • 0034696680 scopus 로고    scopus 로고
    • Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 Å resolution: mechanistic implications
    • Howard B.R., Endrizzi J.A., and Remington S.J. Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 Å resolution: mechanistic implications. Biochemistry 39 (2000) 3156-3168
    • (2000) Biochemistry , vol.39 , pp. 3156-3168
    • Howard, B.R.1    Endrizzi, J.A.2    Remington, S.J.3
  • 26
    • 0041510314 scopus 로고    scopus 로고
    • Structure of the Escherichia coli malate synthase G:pyruvate:acetyl-coenzyme A abortive ternary complex at 1.95 Å resolution
    • Anstrom D.M., Kallio K., and Remington S.J. Structure of the Escherichia coli malate synthase G:pyruvate:acetyl-coenzyme A abortive ternary complex at 1.95 Å resolution. Protein Sci. 12 (2003) 1822-1832
    • (2003) Protein Sci. , vol.12 , pp. 1822-1832
    • Anstrom, D.M.1    Kallio, K.2    Remington, S.J.3
  • 27
    • 33746481387 scopus 로고    scopus 로고
    • The product complex of M. tuberculosis malate synthase revisited
    • Anstrom D.M., and Remington S.J. The product complex of M. tuberculosis malate synthase revisited. Protein Sci. 15 (2006) 2002-2007
    • (2006) Protein Sci. , vol.15 , pp. 2002-2007
    • Anstrom, D.M.1    Remington, S.J.2
  • 28
    • 0033605891 scopus 로고    scopus 로고
    • The crystal structure of Escherichia coli class II fructose-1,6- bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity
    • Hall D.R., Leonard G.A., Reed C.D., Watt C.I., Berry A., and Hunter W.N. The crystal structure of Escherichia coli class II fructose-1,6- bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity. J. Mol. Biol. 287 (1999) 383-394
    • (1999) J. Mol. Biol. , vol.287 , pp. 383-394
    • Hall, D.R.1    Leonard, G.A.2    Reed, C.D.3    Watt, C.I.4    Berry, A.5    Hunter, W.N.6
  • 29
    • 0036290392 scopus 로고    scopus 로고
    • A functional role for a flexible loop containing Glu182 in the class II fructose- 1,6-bisphosphate aldolase from Escherichia coli
    • Zgiby S., Plater A.R., Bates M.A., Thomson G.J., and Berry A. A functional role for a flexible loop containing Glu182 in the class II fructose- 1,6-bisphosphate aldolase from Escherichia coli. J. Mol. Biol. 315 (2002) 131-140
    • (2002) J. Mol. Biol. , vol.315 , pp. 131-140
    • Zgiby, S.1    Plater, A.R.2    Bates, M.A.3    Thomson, G.J.4    Berry, A.5
  • 30
    • 33747064113 scopus 로고    scopus 로고
    • Expression, purification and preliminary crystallographic analysis of 2,4-dihydroxy-hepta- 2-ene 1,7-dioate aldolase (HpcH) from Escherichia coli C
    • Rea D., Fülöp V., Bugg T.D.H., and Roper D.I. Expression, purification and preliminary crystallographic analysis of 2,4-dihydroxy-hepta- 2-ene 1,7-dioate aldolase (HpcH) from Escherichia coli C. Acta Crystallog. sect. F 61 (2005) 821-824
    • (2005) Acta Crystallog. sect. F , vol.61 , pp. 821-824
    • Rea, D.1    Fülöp, V.2    Bugg, T.D.H.3    Roper, D.I.4
  • 31
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 34
    • 0030809260 scopus 로고    scopus 로고
    • wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models
    • Perrakis A., Sixma T.K., Wilson K.S., and Lamzin V.S. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. Acta Crystallog. sect. D 53 (1997) 448-455
    • (1997) Acta Crystallog. sect. D , vol.53 , pp. 448-455
    • Perrakis, A.1    Sixma, T.K.2    Wilson, K.S.3    Lamzin, V.S.4
  • 35
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
    • (1997) Acta Crystallog. sect. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 36
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
    • (1991) Acta Crystallog. sect. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 37
    • 0026244229 scopus 로고
    • MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
    • Kraulis P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24 (1991) 946-950
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.1
  • 38
    • 0030729838 scopus 로고    scopus 로고
    • An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
    • Esnouf R.M. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. 15 (1997) 133-138
    • (1997) J. Mol. Graph. , vol.15 , pp. 133-138
    • Esnouf, R.M.1
  • 39
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
    • (1994) Nucl. Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 40
    • 84944812409 scopus 로고
    • Improved Fourier coefficients for maps using phases from partial structures with errors
    • Read R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallog. sect. A 42 (1986) 140-149
    • (1986) Acta Crystallog. sect. A , vol.42 , pp. 140-149
    • Read, R.J.1
  • 41
    • 0026597444 scopus 로고
    • Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355 (1992) 472-475
    • (1992) Nature , vol.355 , pp. 472-475
    • Brünger, A.T.1
  • 42
    • 0033106268 scopus 로고    scopus 로고
    • Remarks about protein structure precision
    • Cruickshank D.W. Remarks about protein structure precision. Acta Crystallog. sect. D 55 (1999) 583-601
    • (1999) Acta Crystallog. sect. D , vol.55 , pp. 583-601
    • Cruickshank, D.W.1


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