-
1
-
-
33750460925
-
Oxygenases and dehalogenases: molecular approaches to efficient degradation of chlorinated environmental pollutants
-
Furukawa K. Oxygenases and dehalogenases: molecular approaches to efficient degradation of chlorinated environmental pollutants. Biosci. Biotechnol. Biochem. 70 (2006) 2335-2348
-
(2006)
Biosci. Biotechnol. Biochem.
, vol.70
, pp. 2335-2348
-
-
Furukawa, K.1
-
2
-
-
0036889485
-
Transposition of DEH, a broad-host-range transposon flanked by ISPpu12, in Pseudomonas putida is associated with genomic rearrangements and dehalogenase gene silencing
-
Weightman A.J., Topping A.W., Hill K.E., Lee L.L., Sakai K., Slater J.H., and Thomas A.W. Transposition of DEH, a broad-host-range transposon flanked by ISPpu12, in Pseudomonas putida is associated with genomic rearrangements and dehalogenase gene silencing. J. Bacteriol. 184 (2002) 6581-6591
-
(2002)
J. Bacteriol.
, vol.184
, pp. 6581-6591
-
-
Weightman, A.J.1
Topping, A.W.2
Hill, K.E.3
Lee, L.L.4
Sakai, K.5
Slater, J.H.6
Thomas, A.W.7
-
3
-
-
0032909021
-
Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families
-
Hill K.E., Marchesi J.R., and Weightman A.J. Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. J. Bacteriol. 181 (1999) 2535-2547
-
(1999)
J. Bacteriol.
, vol.181
, pp. 2535-2547
-
-
Hill, K.E.1
Marchesi, J.R.2
Weightman, A.J.3
-
5
-
-
0029786674
-
Crystal structure of l-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold
-
Hisano T., Hata Y., Fujii T., Liu J.Q., Kurihara T., Esaki N., and Soda K. Crystal structure of l-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold. J. Biol. Chem. 271 (1996) 20322-20330
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 20322-20330
-
-
Hisano, T.1
Hata, Y.2
Fujii, T.3
Liu, J.Q.4
Kurihara, T.5
Esaki, N.6
Soda, K.7
-
6
-
-
0029006127
-
Comprehensive site-directed mutagenesis of l-2-halo acid dehalogenase to probe catalytic amino acid residues
-
Kurihara T., Liu J.Q., Nardi-Dei V., Koshikawa H., Esaki N., and Soda K. Comprehensive site-directed mutagenesis of l-2-halo acid dehalogenase to probe catalytic amino acid residues. J. Biochem. 117 (1995) 1317-1322
-
(1995)
J. Biochem.
, vol.117
, pp. 1317-1322
-
-
Kurihara, T.1
Liu, J.Q.2
Nardi-Dei, V.3
Koshikawa, H.4
Esaki, N.5
Soda, K.6
-
8
-
-
0035899924
-
Mutagenic analysis of the conserved residues in dehalogenase IVa of Burkholderia cepacia MBA4
-
Pang B.C., and Tsang J.S. Mutagenic analysis of the conserved residues in dehalogenase IVa of Burkholderia cepacia MBA4. FEMS Microbiol. Lett. 204 (2001) 135-140
-
(2001)
FEMS Microbiol. Lett.
, vol.204
, pp. 135-140
-
-
Pang, B.C.1
Tsang, J.S.2
-
9
-
-
0031455377
-
Three-dimensional structure of l-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate
-
Ridder I.S., Rozeboom H.J., Kalk K.H., Janssen D.B., and Dijkstra B.W. Three-dimensional structure of l-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate. J. Biol. Chem. 272 (1997) 33015-33022
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 33015-33022
-
-
Ridder, I.S.1
Rozeboom, H.J.2
Kalk, K.H.3
Janssen, D.B.4
Dijkstra, B.W.5
-
10
-
-
34047138335
-
Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4
-
Schmidberger J.W., Wilce J.A., Tsang J.S., and Wilce M.C. Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4. J. Mol. Biol. 368 (2007) 706-717
-
(2007)
J. Mol. Biol.
, vol.368
, pp. 706-717
-
-
Schmidberger, J.W.1
Wilce, J.A.2
Tsang, J.S.3
Wilce, M.C.4
-
11
-
-
0033863733
-
Identification of the dimerization domain of dehalogenase IVa of Burkholderia cepacia MBA4
-
Tsang J.S., and Pang B.C. Identification of the dimerization domain of dehalogenase IVa of Burkholderia cepacia MBA4. Appl. Environ. Microbiol. 66 (2000) 3180-3186
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 3180-3186
-
-
Tsang, J.S.1
Pang, B.C.2
-
12
-
-
0032510975
-
Crystal structures of reaction intermediates of l-2-haloacid dehalogenase and implications for the reaction mechanism
-
Li Y.F., Hata Y., Fujii T., Hisano T., Nishihara M., Kurihara T., and Esaki N. Crystal structures of reaction intermediates of l-2-haloacid dehalogenase and implications for the reaction mechanism. J. Biol. Chem. 273 (1998) 15035-15044
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 15035-15044
-
-
Li, Y.F.1
Hata, Y.2
Fujii, T.3
Hisano, T.4
Nishihara, M.5
Kurihara, T.6
Esaki, N.7
-
13
-
-
0032724654
-
Crystal structures of intermediates in the dehalogenation of haloalkanoates by l-2-haloacid dehalogenase
-
Ridder I.S., Rozeboom H.J., Kalk K.H., and Dijkstra B.W. Crystal structures of intermediates in the dehalogenation of haloalkanoates by l-2-haloacid dehalogenase. J. Biol. Chem. 274 (1999) 30672-30678
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 30672-30678
-
-
Ridder, I.S.1
Rozeboom, H.J.2
Kalk, K.H.3
Dijkstra, B.W.4
-
14
-
-
0019915696
-
Stereospecificity of 2-monochloropropionate dehalogenation by the two dehalogenases of Pseudomonas putida PP3: evidence for two different dehalogenation mechanisms
-
Weightman A.J., Weightman A.L., and Slater J.H. Stereospecificity of 2-monochloropropionate dehalogenation by the two dehalogenases of Pseudomonas putida PP3: evidence for two different dehalogenation mechanisms. J. Gen. Microbiol. 128 (1982) 1755-1762
-
(1982)
J. Gen. Microbiol.
, vol.128
, pp. 1755-1762
-
-
Weightman, A.J.1
Weightman, A.L.2
Slater, J.H.3
-
15
-
-
0030435054
-
Cloning and nucleotide sequence of a d,l-haloalkanoic acid dehalogenase encoding gene from Alcaligenes xylosoxidans ssp. denitrificans ABIV
-
Brokamp A., Happe B., and Schmidt F.R. Cloning and nucleotide sequence of a d,l-haloalkanoic acid dehalogenase encoding gene from Alcaligenes xylosoxidans ssp. denitrificans ABIV. Biodegradation 7 (1996) 383-396
-
(1996)
Biodegradation
, vol.7
, pp. 383-396
-
-
Brokamp, A.1
Happe, B.2
Schmidt, F.R.3
-
16
-
-
0030760868
-
Bacterial dl2-haloacid dehalogenase from Pseudomonas sp. strain 113: gene cloning and structural comparison with d- and l-2-haloacid dehalogenases
-
Nardi-Dei V., Kurihara T., Park C., Esaki N., and Soda K. Bacterial dl2-haloacid dehalogenase from Pseudomonas sp. strain 113: gene cloning and structural comparison with d- and l-2-haloacid dehalogenases. J. Bacteriol. 179 (1997) 4232-4238
-
(1997)
J. Bacteriol.
, vol.179
, pp. 4232-4238
-
-
Nardi-Dei, V.1
Kurihara, T.2
Park, C.3
Esaki, N.4
Soda, K.5
-
17
-
-
0033597883
-
dl-2-Haloacid dehalogenase from Pseudomonas sp. 113 is a new class of dehalogenase catalyzing hydrolytic dehalogenation not involving enzyme-substrate ester intermediate
-
Nardi-Dei V., Kurihara T., Park C., Miyagi M., Tsunasawa S., Soda K., and Esaki N. dl-2-Haloacid dehalogenase from Pseudomonas sp. 113 is a new class of dehalogenase catalyzing hydrolytic dehalogenation not involving enzyme-substrate ester intermediate. J. Biol. Chem. 274 (1999) 20977-20981
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 20977-20981
-
-
Nardi-Dei, V.1
Kurihara, T.2
Park, C.3
Miyagi, M.4
Tsunasawa, S.5
Soda, K.6
Esaki, N.7
-
18
-
-
0017135529
-
Enzyme evolution in a microbial community growing on the herbicide Dalapon
-
Senior E., Bull A.T., and Slater J.H. Enzyme evolution in a microbial community growing on the herbicide Dalapon. Nature 263 (1976) 476-479
-
(1976)
Nature
, vol.263
, pp. 476-479
-
-
Senior, E.1
Bull, A.T.2
Slater, J.H.3
-
19
-
-
0032104477
-
How far divergent evolution goes in proteins
-
Murzin A.G. How far divergent evolution goes in proteins. Curr. Opin. Struct. Biol. 8 (1998) 380-387
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 380-387
-
-
Murzin, A.G.1
-
20
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
21
-
-
33847142225
-
CAVER: a new tool to explore routes from protein clefts, pockets and cavities
-
Petrek M., Otyepka M., Banas P., Kosinova P., Koca J., and Damborsky J. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7 (2006) 316
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 316
-
-
Petrek, M.1
Otyepka, M.2
Banas, P.3
Kosinova, P.4
Koca, J.5
Damborsky, J.6
-
22
-
-
0017881332
-
The alpha-helix dipole and the properties of proteins
-
Hol W.G., van Duijnen P.T., and Berendsen H.J. The alpha-helix dipole and the properties of proteins. Nature 273 (1978) 443-446
-
(1978)
Nature
, vol.273
, pp. 443-446
-
-
Hol, W.G.1
van Duijnen, P.T.2
Berendsen, H.J.3
-
24
-
-
12144289984
-
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner R.A., Banks J.L., Murphy R.B., Halgren T.A., Klicic J.J., Mainz D.T., et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 47 (2004) 1739-1749
-
(2004)
J. Med. Chem.
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
-
25
-
-
0027337615
-
Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase
-
Verschueren K.H., Seljee F., Rozeboom H.J., Kalk K.H., and Dijkstra B.W. Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase. Nature 363 (1993) 693-698
-
(1993)
Nature
, vol.363
, pp. 693-698
-
-
Verschueren, K.H.1
Seljee, F.2
Rozeboom, H.J.3
Kalk, K.H.4
Dijkstra, B.W.5
-
26
-
-
0037117757
-
Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition
-
Oakley A.J., Prokop Z., Bohac M., Kmunicek J., Jedlicka T., Monincova M., et al. Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition. Biochemistry 41 (2002) 4847-4855
-
(2002)
Biochemistry
, vol.41
, pp. 4847-4855
-
-
Oakley, A.J.1
Prokop, Z.2
Bohac, M.3
Kmunicek, J.4
Jedlicka, T.5
Monincova, M.6
-
27
-
-
0942301386
-
Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 Å resolution: dynamics of catalytic residues
-
Oakley A.J., Klvana M., Otyepka M., Nagata Y., Wilce M.C., and Damborsky J. Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 Å resolution: dynamics of catalytic residues. Biochemistry 43 (2004) 870-878
-
(2004)
Biochemistry
, vol.43
, pp. 870-878
-
-
Oakley, A.J.1
Klvana, M.2
Otyepka, M.3
Nagata, Y.4
Wilce, M.C.5
Damborsky, J.6
-
28
-
-
0041823656
-
Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates
-
Streltsov V.A., Prokop Z., Damborsky J., Nagata Y., Oakley A., and Wilce M.C. Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates. Biochemistry 42 (2003) 10104-10112
-
(2003)
Biochemistry
, vol.42
, pp. 10104-10112
-
-
Streltsov, V.A.1
Prokop, Z.2
Damborsky, J.3
Nagata, Y.4
Oakley, A.5
Wilce, M.C.6
-
30
-
-
0025816929
-
Survival of Alcaligenes xylosoxidans degrading 2,2-dichloropropionate and horizontal transfer of its halidohydrolase gene in a soil microcosm
-
Brokamp A., and Schmidt F.R. Survival of Alcaligenes xylosoxidans degrading 2,2-dichloropropionate and horizontal transfer of its halidohydrolase gene in a soil microcosm. Curr. Microbiol. 22 (1991) 299-306
-
(1991)
Curr. Microbiol.
, vol.22
, pp. 299-306
-
-
Brokamp, A.1
Schmidt, F.R.2
-
31
-
-
0019973155
-
Bacterial assimilation of d- and l-2-chloropropionates and occurrence of a new dehalogenase
-
Motosugi K., Esaki N., and Soda K. Bacterial assimilation of d- and l-2-chloropropionates and occurrence of a new dehalogenase. Arch. Microbiol. 131 (1982) 179-183
-
(1982)
Arch. Microbiol.
, vol.131
, pp. 179-183
-
-
Motosugi, K.1
Esaki, N.2
Soda, K.3
-
32
-
-
33646554554
-
Mechanism of the reaction catalyzed by dl2-haloacid dehalogenase as determined from kinetic isotope effects
-
Papajak E., Kwiecien R.A., Rudzinski J., Sicinska D., Kaminski R., Szatkowski L., et al. Mechanism of the reaction catalyzed by dl2-haloacid dehalogenase as determined from kinetic isotope effects. Biochemistry 45 (2006) 6012-6017
-
(2006)
Biochemistry
, vol.45
, pp. 6012-6017
-
-
Papajak, E.1
Kwiecien, R.A.2
Rudzinski, J.3
Sicinska, D.4
Kaminski, R.5
Szatkowski, L.6
-
33
-
-
0026762899
-
Cloning and partial sequencing of an operon encoding two Pseudomonas putida haloalkanoate dehalogenases of opposite stereospecificity
-
Barth P.T., Bolton L., and Thomson J.C. Cloning and partial sequencing of an operon encoding two Pseudomonas putida haloalkanoate dehalogenases of opposite stereospecificity. J. Bacteriol. 174 (1992) 2612-2619
-
(1992)
J. Bacteriol.
, vol.174
, pp. 2612-2619
-
-
Barth, P.T.1
Bolton, L.2
Thomson, J.C.3
-
34
-
-
41149177675
-
-
Leslie, A. G. W. (1992). Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newslett. Protein Crystallogr. 26.
-
Leslie, A. G. W. (1992). Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newslett. Protein Crystallogr. 26.
-
-
-
-
37
-
-
0036848846
-
Automated structure solution, density modification and model building
-
Terwilliger T.C. Automated structure solution, density modification and model building. Acta Crystallogr., Sect. D: Biol. Crystallogr. 58 (2002) 1937-1940
-
(2002)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.58
, pp. 1937-1940
-
-
Terwilliger, T.C.1
-
38
-
-
33748337934
-
The Buccaneer software for automated model building.1. Tracing protein chains
-
Cowtan K. The Buccaneer software for automated model building.1. Tracing protein chains. Acta Crystallogr., Sect. D: Biol. Crystallogr. 62 (2006) 1002-1011
-
(2006)
Acta Crystallogr., Sect. D: Biol. Crystallogr.
, vol.62
, pp. 1002-1011
-
-
Cowtan, K.1
-
41
-
-
0032964481
-
Automated protein model building combined with iterative structure refinement
-
Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6 (1999) 458-463
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 458-463
-
-
Perrakis, A.1
Morris, R.2
Lamzin, V.S.3
-
42
-
-
0037441653
-
Structure validation by Calpha geometry: phi, psi and Cbeta deviation
-
Lovell S.C., Davis I.W., Arendall III W.B., de Bakker P.I., Word J.M., Prisant M.G., et al. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50 (2003) 437-450
-
(2003)
Proteins
, vol.50
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall III, W.B.3
de Bakker, P.I.4
Word, J.M.5
Prisant, M.G.6
-
43
-
-
0028838717
-
Threading a database of protein cores
-
Madej T., Gibrat J.F., and Bryant S.H. Threading a database of protein cores. Proteins 23 (1995) 356-369
-
(1995)
Proteins
, vol.23
, pp. 356-369
-
-
Madej, T.1
Gibrat, J.F.2
Bryant, S.H.3
-
44
-
-
3242889058
-
ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures
-
Chang D.T., Chen C.Y., Chung W.C., Oyang Y.J., Juan H.F., and Huang H.C. ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures. Nucleic Acids Res. 32 (2004) W76-W82
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Chang, D.T.1
Chen, C.Y.2
Chung, W.C.3
Oyang, Y.J.4
Juan, H.F.5
Huang, H.C.6
-
45
-
-
0028871926
-
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
-
46
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
47
-
-
0032961270
-
ESPript: analysis of multiple sequence alignments in PostScript
-
Gouet P., Courcelle E., Stuart D.I., and Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15 (1999) 305-308
-
(1999)
Bioinformatics
, vol.15
, pp. 305-308
-
-
Gouet, P.1
Courcelle, E.2
Stuart, D.I.3
Metoz, F.4
-
48
-
-
13544251502
-
The case for open-source software in drug discovery
-
DeLano W.L. The case for open-source software in drug discovery. Drug Discov. Today 10 (2005) 213-217
-
(2005)
Drug Discov. Today
, vol.10
, pp. 213-217
-
-
DeLano, W.L.1
-
49
-
-
0035964342
-
Electrostatics of nanosystems: application to microtubules and the ribosome
-
Baker N.A., Sept D., Joseph S., Holst M.J., and McCammon J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98 (2001) 10037-10041
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
50
-
-
33847142225
-
CAVER: a new tool to explore routes from protein clefts, pockets and cavities
-
Petrek M., Otyepka M., Banas P., Kosinova P., Koca J., and Damborsky J. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7 (2006) 316
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 316
-
-
Petrek, M.1
Otyepka, M.2
Banas, P.3
Kosinova, P.4
Koca, J.5
Damborsky, J.6
-
51
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E., and Henrick K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372 (2007) 774-797
-
(2007)
J. Mol. Biol.
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
|