-
1
-
-
14244272868
-
phenix: building new software for automated crystallographic structure determination
-
Adams, P., Grosse-Kunstleve, R., Hung, L.-W., Ioerger, T., McCoy, A., Moriarty, N., etal. (2002) phenix: building new software for automated crystallographic structure determination. Acta Crystallogr D58: 1948-1954.
-
(2002)
Acta Crystallogr
, vol.58
, pp. 1948-1954
-
-
Adams, P.1
Grosse-Kunstleve, R.2
Hung, L.-W.3
Ioerger, T.4
McCoy, A.5
Moriarty, N.6
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schaffer, A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
5
-
-
0023032156
-
4-Hydroxyphenylpyruvate dioxygenase is an iron-tyrosinate protein
-
Bradley, F., Lindstedt, S., Lipscomb, J., Que, L., Roe, A., and Rundgren, M. (1986) 4-Hydroxyphenylpyruvate dioxygenase is an iron-tyrosinate protein. J Biol Chem 261: 11693-11696.
-
(1986)
J Biol Chem
, vol.261
, pp. 11693-11696
-
-
Bradley, F.1
Lindstedt, S.2
Lipscomb, J.3
Que, L.4
Roe, A.5
Rundgren, M.6
-
6
-
-
0028244448
-
Phylogenetic evidence for transfer of pentachlorophenol-mineralizing Rhodococcus chlorophenolicus PCP-I(T) to the genus Mycobacterium
-
Briglia, M., Eggen, R., Van Elsas, D., and De Vos, W. (1994) Phylogenetic evidence for transfer of pentachlorophenol-mineralizing Rhodococcus chlorophenolicus PCP-I(T) to the genus Mycobacterium. Int J Syst Bacteriol 44: 494-498.
-
(1994)
Int J Syst Bacteriol
, vol.44
, pp. 494-498
-
-
Briglia, M.1
Eggen, R.2
Van Elsas, D.3
De Vos, W.4
-
7
-
-
0036718377
-
Organization and regulation of pentachlorophenol-degrading genes in Sphingobium chlorophenolicum ATCC 39723
-
Cai, M., and Xun, L. (2002) Organization and regulation of pentachlorophenol-degrading genes in Sphingobium chlorophenolicum ATCC 39723. J Bacteriol 184: 4672-4680.
-
(2002)
J Bacteriol
, vol.184
, pp. 4672-4680
-
-
Cai, M.1
Xun, L.2
-
8
-
-
0022240851
-
Microbial removal of pentachlorophenol from soil using a Flavobacterium
-
Crawford, R., and Mohn, W. (1985) Microbial removal of pentachlorophenol from soil using a Flavobacterium. Enzyme Microb Technol 7: 617-620.
-
(1985)
Enzyme Microb Technol
, vol.7
, pp. 617-620
-
-
Crawford, R.1
Mohn, W.2
-
9
-
-
0019511605
-
Environmental chemistry of pentachlorophenol
-
Crosby, D. (1981) Environmental chemistry of pentachlorophenol. Pure Appl Chem 53: 1052-1080.
-
(1981)
Pure Appl Chem
, vol.53
, pp. 1052-1080
-
-
Crosby, D.1
-
10
-
-
0037215599
-
A previously unrecognized step in pentachlorophenol degradation in Sphingobium chlorophenolicum is catalyzed by tetrachlorobenzoquinone reductase (PcpD)
-
Dai, M., Rogers, J., Warner, J., and Copley, S. (2003) A previously unrecognized step in pentachlorophenol degradation in Sphingobium chlorophenolicum is catalyzed by tetrachlorobenzoquinone reductase (PcpD). J Bacteriol 185: 302-310.
-
(2003)
J Bacteriol
, vol.185
, pp. 302-310
-
-
Dai, M.1
Rogers, J.2
Warner, J.3
Copley, S.4
-
11
-
-
77949535720
-
Features and development of Coot
-
Emsley, P., Lohkamp, B., Scott, W.G., and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486-501.
-
(2010)
Acta Crystallogr D Biol Crystallogr
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
12
-
-
0001828796
-
The 2,3,7,8-trtrachlorodibenzo-para-dioxin problem: a review
-
Firestone, D. (1978) The 2, 3, 7, 8-trtrachlorodibenzo-para-dioxin problem: a review. Stockh Ecol Bull 27: 39-52.
-
(1978)
Stockh Ecol Bull
, vol.27
, pp. 39-52
-
-
Firestone, D.1
-
13
-
-
0028245047
-
Transfer of polychlorophenol-degrading Rhodococcus chlorophenolicus (Apajalahti 1986) to the genus Mycobacterium as Mycobacterium chlorophenolicum comb. nov.
-
Häggblom, M., Nohynek, L., Palleroni, N., Kronqvist, K., Nurmiaho-Lassila, E., Salkinoja-Salonen, M., etal. (1994) Transfer of polychlorophenol-degrading Rhodococcus chlorophenolicus (Apajalahti etal. 1986) to the genus Mycobacterium as Mycobacterium chlorophenolicum comb. nov. J Syst Bacteriol 44: 485-493.
-
(1994)
J Syst Bacteriol
, vol.44
, pp. 485-493
-
-
Häggblom, M.1
Nohynek, L.2
Palleroni, N.3
Kronqvist, K.4
Nurmiaho-Lassila, E.5
Salkinoja-Salonen, M.6
-
14
-
-
0026805891
-
Functional and evolutionary relationships among diverse oxygenases
-
Harayama, S., Kok, M., and Neidle, E. (1992) Functional and evolutionary relationships among diverse oxygenases. Annu Rev Microbiol 46: 565-601.
-
(1992)
Annu Rev Microbiol
, vol.46
, pp. 565-601
-
-
Harayama, S.1
Kok, M.2
Neidle, E.3
-
15
-
-
79961110102
-
Structural and mechanistic comparisons of the metal-binding members of the vicinal oxygen chelate (VOC) superfamily
-
He, P., and Moran, G. (2011) Structural and mechanistic comparisons of the metal-binding members of the vicinal oxygen chelate (VOC) superfamily. J Inorg Biochem 105: 1259-1272.
-
(2011)
J Inorg Biochem
, vol.105
, pp. 1259-1272
-
-
He, P.1
Moran, G.2
-
16
-
-
0033179656
-
Natural formation of chlorinated phenols, dibenzo-p-dioxins, and dibenzofurans in soil of a Douglas fir forest
-
Hoekstra, E., de Weerd, H., de Leer, E., and Brinkman, U. (1999) Natural formation of chlorinated phenols, dibenzo-p-dioxins, and dibenzofurans in soil of a Douglas fir forest. Environ Sci Technol 33: 2543-2549.
-
(1999)
Environ Sci Technol
, vol.33
, pp. 2543-2549
-
-
Hoekstra, E.1
de Weerd, H.2
de Leer, E.3
Brinkman, U.4
-
17
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm, L., and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233: 123-138.
-
(1993)
J Mol Biol
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
18
-
-
0030596529
-
Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures
-
Klabunde, T., Sträter, N., Fröhlich, R., Witzel, H., and Krebs, B. (1996) Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures. J Mol Biol 259: 737-748.
-
(1996)
J Mol Biol
, vol.259
, pp. 737-748
-
-
Klabunde, T.1
Sträter, N.2
Fröhlich, R.3
Witzel, H.4
Krebs, B.5
-
19
-
-
17644413773
-
The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes
-
Koehntop, K., Emerson, J., and Que, L.J. (2005) The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes. J Biol Inorg Chem 10: 87-93.
-
(2005)
J Biol Inorg Chem
, vol.10
, pp. 87-93
-
-
Koehntop, K.1
Emerson, J.2
Que, L.J.3
-
20
-
-
34247534094
-
2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates
-
2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates. Science 316: 453-457.
-
(2007)
Science
, vol.316
, pp. 453-457
-
-
Kovaleva, E.G.1
Lipscomb, J.D.2
-
21
-
-
57049146277
-
Mechanism of extradiol aromatic ring-cleaving dioxygenases
-
Lipscomb, J.D. (2008) Mechanism of extradiol aromatic ring-cleaving dioxygenases. Curr Opin Struct Biol 18: 644-649.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 644-649
-
-
Lipscomb, J.D.1
-
22
-
-
77949261552
-
Determination of the active site of Sphingobium chlorophenolicum 2,6-dichlorohydroquinone dioxygenase (PcpA)
-
Machonkin, T., Holland, P., Smith, K., Liberman, J., Dinescu, A., Cundari, T., and Rocks, S. (2010) Determination of the active site of Sphingobium chlorophenolicum 2, 6-dichlorohydroquinone dioxygenase (PcpA). J Biol Inorg Chem 15: 291-301.
-
(2010)
J Biol Inorg Chem
, vol.15
, pp. 291-301
-
-
Machonkin, T.1
Holland, P.2
Smith, K.3
Liberman, J.4
Dinescu, A.5
Cundari, T.6
Rocks, S.7
-
23
-
-
80054757502
-
Substrate specificity of Sphingobium chlorophenolicum 2,6-dichlorohydroquinone 1,2-dioxygenase
-
Machonkin, T.E., and Doerner, A.E. (2011) Substrate specificity of Sphingobium chlorophenolicum 2, 6-dichlorohydroquinone 1, 2-dioxygenase. Biochemistry 50: 8899-8913.
-
(2011)
Biochemistry
, vol.50
, pp. 8899-8913
-
-
Machonkin, T.E.1
Doerner, A.E.2
-
24
-
-
0029659241
-
Accelerated mineralization of pentachlorophenol in soil upon inoculation with Mycobacterium chlorophenolicum PCP1 and Sphingomonas chlorophenolica RA2
-
Miethling, R., and Karlson, U. (1996) Accelerated mineralization of pentachlorophenol in soil upon inoculation with Mycobacterium chlorophenolicum PCP1 and Sphingomonas chlorophenolica RA2. Appl Environ Microbiol 62: 4361-4366.
-
(1996)
Appl Environ Microbiol
, vol.62
, pp. 4361-4366
-
-
Miethling, R.1
Karlson, U.2
-
25
-
-
0032704711
-
Cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis
-
Miyauchi, K., Adachi, Y., Nagata, Y., and Takagi, M. (1999) Cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis. J Bacteriol 181: 6712-6719.
-
(1999)
J Bacteriol
, vol.181
, pp. 6712-6719
-
-
Miyauchi, K.1
Adachi, Y.2
Nagata, Y.3
Takagi, M.4
-
26
-
-
48149092978
-
Hydroquinone dioxygenase from pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases
-
Moonen, M.J., Synowsky, S.A., van den Berg, W.A., Westphal, A.H., Heck, A.J., van den Heuvel, R.H., etal. (2008) Hydroquinone dioxygenase from pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases. J Bacteriol 190: 5199-5209.
-
(2008)
J Bacteriol
, vol.190
, pp. 5199-5209
-
-
Moonen, M.J.1
van den Synowsky, S.A.2
Berg, W.A.3
Westphal, A.H.4
van den Heck, A.J.5
Heuvel, R.H.6
-
27
-
-
70349932423
-
AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility
-
Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S., and Olson, A.J. (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30: 2785-2791.
-
(2009)
J Comput Chem
, vol.30
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
Sanner, M.F.4
Belew, R.K.5
Goodsell, D.S.6
Olson, A.J.7
-
28
-
-
0032885089
-
PcpA, which is involved in the degradation of pentachlorophenol in Sphingomonas chlorophenolica ATCC39723, is a novel type of ring-cleavage dioxygenase
-
Ohtsubo, Y., Miyauchi, K., Kanda, K., Hatta, T., Kiyohara, H., Senda, T., etal. (1999) PcpA, which is involved in the degradation of pentachlorophenol in Sphingomonas chlorophenolica ATCC39723, is a novel type of ring-cleavage dioxygenase. FEBS Lett 459: 395-598.
-
(1999)
FEBS Lett
, vol.459
, pp. 395-598
-
-
Ohtsubo, Y.1
Miyauchi, K.2
Kanda, K.3
Hatta, T.4
Kiyohara, H.5
Senda, T.6
-
29
-
-
0027204866
-
Characterization of a Flavobacterium glutathione S-transferase gene involved reductive dechlorination
-
Orser, C.S., Dutton, J., Lange, C., Jablonski, P., Xun, L., and Hargis, M. (1993) Characterization of a Flavobacterium glutathione S-transferase gene involved reductive dechlorination. J Bacteriol 175: 2640-2644.
-
(1993)
J Bacteriol
, vol.175
, pp. 2640-2644
-
-
Orser, C.S.1
Dutton, J.2
Lange, C.3
Jablonski, P.4
Xun, L.5
Hargis, M.6
-
30
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326.
-
(1997)
Methods Enzymol
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
31
-
-
0039302669
-
Dioxygen activation by enzymes with mononuclear nonheme iron active sites
-
Que, L., and Ho, R. (1996) Dioxygen activation by enzymes with mononuclear nonheme iron active sites. Chem Rev 96: 2607-2624.
-
(1996)
Chem Rev
, vol.96
, pp. 2607-2624
-
-
Que, L.1
Ho, R.2
-
32
-
-
0022411177
-
Isolation and characterization of Flavobacterium strains that degrade pentachlorophenol
-
Saber, D., and Crawford, R. (1985) Isolation and characterization of Flavobacterium strains that degrade pentachlorophenol. Appl Environ Microbiol 50: 1512-1518.
-
(1985)
Appl Environ Microbiol
, vol.50
, pp. 1512-1518
-
-
Saber, D.1
Crawford, R.2
-
33
-
-
0033397980
-
Python: a programming language for software integration and development
-
Sanner, M. (1999) Python: a programming language for software integration and development. J Mol Graph Model 17: 57-61.
-
(1999)
J Mol Graph Model
, vol.17
, pp. 57-61
-
-
Sanner, M.1
-
34
-
-
0036965765
-
Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase
-
Sato, N., Uragami, Y., Nishizaki, T., Takahashi, Y., Sazaki, G., Sugimoto, K., etal. (2002) Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase. J Mol Biol 321: 621-636.
-
(2002)
J Mol Biol
, vol.321
, pp. 621-636
-
-
Sato, N.1
Uragami, Y.2
Nishizaki, T.3
Takahashi, Y.4
Sazaki, G.5
Sugimoto, K.6
-
35
-
-
0030008087
-
Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102
-
Senda, T., Sugiyama, K., Narita, H., Yamamoto, T., Kimbara, K., Fukuda, M., etal. (1996) Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102. J Mol Biol 255: 735-752.
-
(1996)
J Mol Biol
, vol.255
, pp. 735-752
-
-
Senda, T.1
Sugiyama, K.2
Narita, H.3
Yamamoto, T.4
Kimbara, K.5
Fukuda, M.6
-
36
-
-
77957746479
-
Cloning and characterization of a gene cluster involved in the catabolism of p-nitrophenol from Pseudomonas putida DLL-E4
-
Shen, W., Liu, W., Zhang, J., Tao, J., Deng, H., Cao, H., and Cui, Z. (2010) Cloning and characterization of a gene cluster involved in the catabolism of p-nitrophenol from Pseudomonas putida DLL-E4. Bioresour Technol 101: 7516-7522.
-
(2010)
Bioresour Technol
, vol.101
, pp. 7516-7522
-
-
Shen, W.1
Liu, W.2
Zhang, J.3
Tao, J.4
Deng, H.5
Cao, H.6
Cui, Z.7
-
37
-
-
0029038688
-
X-ray absorption spectroscopic studies of the Fe(II) active site of catechol 2,3-dioxygenase. Implications for the extradiol cleavage mechanism
-
Shu, L., Chiou, Y.M., Orville, A.M., Miller, M.A., Lipscomb, J.D., and Que, L., Jr. (1995) X-ray absorption spectroscopic studies of the Fe(II) active site of catechol 2, 3-dioxygenase. Implications for the extradiol cleavage mechanism. Biochemistry 34: 6649-6659.
-
(1995)
Biochemistry
, vol.34
, pp. 6649-6659
-
-
Shu, L.1
Chiou, Y.M.2
Orville, A.M.3
Miller, M.A.4
Lipscomb, J.D.5
Que Jr., L.6
-
38
-
-
9944235885
-
Highly accurate coupled cluster potential energy curves for the benzene dimer: sandwich, T-shaped, and parallel-displaced configurations
-
Sinnokrot, M., and Sherril, C. (2004) Highly accurate coupled cluster potential energy curves for the benzene dimer: sandwich, T-shaped, and parallel-displaced configurations. J Phys Chem A 108: 10200-10207.
-
(2004)
J Phys Chem A
, vol.108
, pp. 10200-10207
-
-
Sinnokrot, M.1
Sherril, C.2
-
39
-
-
77955512534
-
Thermodynamic and kinetic considerations for the reaction of semiquinone radicals to form superoxide and hydrogen peroxide
-
Song, Y., and Buettner, G. (2010) Thermodynamic and kinetic considerations for the reaction of semiquinone radicals to form superoxide and hydrogen peroxide. Free Radic Biol Med 49: 919-962.
-
(2010)
Free Radic Biol Med
, vol.49
, pp. 919-962
-
-
Song, Y.1
Buettner, G.2
-
40
-
-
80355135227
-
Sphingobium chlorophenolicum dichlorohydroquinone dioxygenase (PcpA) is alkaline resistant and thermally stable
-
Sun, W., Sammynaiken, R., Chen, L., Maley, J., Schatte, G., Zhou, Y., and Yang, J. (2011) Sphingobium chlorophenolicum dichlorohydroquinone dioxygenase (PcpA) is alkaline resistant and thermally stable. Int J Biol Sci 7: 1171-1179.
-
(2011)
Int J Biol Sci
, vol.7
, pp. 1171-1179
-
-
Sun, W.1
Sammynaiken, R.2
Chen, L.3
Maley, J.4
Schatte, G.5
Zhou, Y.6
Yang, J.7
-
41
-
-
0036135280
-
Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system
-
Tiirola, M., Männistö, M., Puhakka, J., and Kulomaa, M. (2002) Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system. Appl Environ Microbiol 68: 173-180.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 173-180
-
-
Tiirola, M.1
Männistö, M.2
Puhakka, J.3
Kulomaa, M.4
-
42
-
-
76249124150
-
Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:FAD oxidoreductase (TftC) of Burkholderia cepacia AC1100
-
Webb, B.N., Ballinger, J.W., Kim, E., Belchik, S.M., Lam, K.S., Youn, B., etal. (2010) Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:FAD oxidoreductase (TftC) of Burkholderia cepacia AC1100. J Biol Chem 285: 2014-2027.
-
(2010)
J Biol Chem
, vol.285
, pp. 2014-2027
-
-
Webb, B.N.1
Ballinger, J.W.2
Kim, E.3
Belchik, S.M.4
Lam, K.S.5
Youn, B.6
-
43
-
-
0025733737
-
Purification and properties of pentachlorophenol hydroxylase, a flavoprotein from Flavobacterium sp. strain ATCC 39723
-
Xun, L., and Orser, C.S. (1991) Purification and properties of pentachlorophenol hydroxylase, a flavoprotein from Flavobacterium sp. strain ATCC 39723. J Bacteriol 173: 4447-4453.
-
(1991)
J Bacteriol
, vol.173
, pp. 4447-4453
-
-
Xun, L.1
Orser, C.S.2
-
44
-
-
0033590113
-
Characterization of 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA) of Sphingomonas chlorophenolica ATCC 39723
-
Xun, L., Bohuslavek, J., and Cai, M. (1999) Characterization of 2, 6-dichloro-p-hydroquinone 1, 2-dioxygenase (PcpA) of Sphingomonas chlorophenolica ATCC 39723. Biochem Biophys Res Commun 266: 322-325.
-
(1999)
Biochem Biophys Res Commun
, vol.266
, pp. 322-325
-
-
Xun, L.1
Bohuslavek, J.2
Cai, M.3
-
45
-
-
78149409239
-
Characterization of MnpC, a hydroquinone dioxygenase likely involved in the meta-nitrophenol degradation by Cupriavidus necator JMP134
-
Yin, Y., and Zhou, N.Y. (2010) Characterization of MnpC, a hydroquinone dioxygenase likely involved in the meta-nitrophenol degradation by Cupriavidus necator JMP134. Curr Microbiol 61: 471-476.
-
(2010)
Curr Microbiol
, vol.61
, pp. 471-476
-
-
Yin, Y.1
Zhou, N.Y.2
|