Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1

BMC Structural Biology

Volumn 7, Issue , 2007, Pages

  Ferraro, Daniel J ^a   Brown, Eric N ^a   Yu, Chi Li ^a   Parales, Rebecca E ^b   Gibson, David T ^a   Ramaswamy, S ^a  

^a UNIVERSITY OF IOWA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUND; BENZO[A]PYRENE; BIPHENYL 3,3 DIOXYGENASE; CHRYSENE; FERREDOXIN; HEME OXYGENASE; IRON SULFUR PROTEIN; NAPHTHALENE DERIVATIVE; OXIDOREDUCTASE; OXYGENASE; UNCLASSIFIED DRUG; BIPHENYL 2,3 DIOXYGENASE; BIPHENYL-2,3-DIOXYGENASE; HISTIDINE; IRON;

ARTICLE; BACTERIAL STRAIN; BEIJERINCKIA; BINDING SITE; COMPARATIVE STUDY; CONTROLLED STUDY; CRYSTAL STRUCTURE; ELECTRON; ENZYME BINDING; ENZYME STRUCTURE; NONHUMAN; OXIDATION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; SEQUENCE ANALYSIS; SPHINGOBIUM YANOIKUYAE; SPHINGOMONAS; CHEMISTRY; GENETICS; KINETICS; METABOLISM; PROTEIN BINDING; SPHINGOBACTERIUM;

BACTERIA (MICROORGANISMS); BEIJERINCKIA SP.; PSEUDOMONAS SP.; SPHINGOBIUM YANOIKUYAE;

BINDING SITES; FERREDOXINS; HISTIDINE; IRON; IRON-SULFUR PROTEINS; KINETICS; OXYGENASES; PROTEIN BINDING; SPHINGOBACTERIUM;

EID: 34047222146     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-7-10     Document Type: Article

References (67)

1. Reclassification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Beijerinckia sp. strain B1, as Sphingomonas yanoikuyae by fatty acid analysis, protein pattern analysis, DNA-DNA hybridization, and 16S ribosomal DNA sequencing. AA Khan RF Wang WW Cao W Franklin CE Cerniglia, Int J Syst Bacteriol 1996 46 2 466 469 8934904
2. Oxidation of biphenyl by a Beijerinckia species. DT Gibson RL Roberts MC Wells VM Kobal, Biochem Biophys Res Commun 1973 50 2 211 219 10.1016/0006-291X(73)90828-0 4689045
3. Beijerinckia sp strain B1: a strain by any other name. DT Gibson, J Ind Microbiol Biotechnol 1999 23 4-5 284 293 10.1038/sj.jim.2900715 11423945
4. Molecular cloning and expression of genes encoding a novel dioxygenase involved in low- and high-molecular-weight polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. SJ Kim O Kweon JP Freeman RC Jones MD Adjei JW Jhoo RD Edmondson CE Cerniglia, Appl Environ Microbiol 2006 72 2 1045 1054 16461648 10.1128/AEM.72.2.1045-1054.2006
5. Purification and characterization of an arene cis-dihydrodiol dehydrogenase endowed with broad substrate specificity toward polycyclic aromatic hydrocarbon dihydrodiols. Y Jouanneau C Meyer, Appl Environ Microbiol 2006 72 7 4726 4734 16820465 10.1128/AEM.00395-06
6. Identification and functional analysis of two aromatic-ring-hydroxylating dioxygenases from a Sphingomonas strain that degrades various polycyclic aromatic hydrocarbons. S Demaneche C Meyer J Micoud M Louwagie JC Willison Y Jouanneau, Appl Environ Microbiol 2004 70 11 6714 6725 15528538 10.1128/AEM.70.11.6714-6725.2004
7. Characterization of a naphthalene dioxygenase endowed with an exceptionally broad substrate specificity toward polycyclic aromatic hydrocarbons. Y Jouanneau C Meyer J Jakoncic V Stojanoff J Gaillard, Biochemistry 2006 45 40 12380 12391 10.1021/bi0611311 17014090
8. Oxidation of the carcinogens benzo[a]pyrene and benzo[a]anthracene to dihydrodiols by a bacterium. DT Gibson V Mahadevan DM Jerina H Yogi HJ Yeh, Science 1975 189 4199 295 297 10.1126/science.1145203 1145203
9. Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1. GJ Zylstra E Kim, J Ind Microbiol Biotechnol 1997 19 5-6 408 414 10.1038/sj.jim.2900475
10. Functional analysis of genes involved in biphenyl, naphthalene, phenanthrene, and m-xylene degradation by Sphingomonas yanoikuyae B1. E Kim GJ Zylstra, J Ind Microbiol Biotechnol 1999 23 4-5 294 302 10.1038/sj.jim.2900724 11423946
11. Purification, characterization, and crystallization of the components of a biphenyl dioxygenase system from Sphingobium yanoikuyae B1. CL Yu W Liu DJ Ferraro EN Brown S Ramaswamy RE Parales DT Gibson, J Ind Microbiol Biotechnol 2007 34 4 311 24 10.1007/s10295-006-0199-8 17211635
12. Catabolic role of a three-component salicylate oxygenase from Sphingomonas yanoikuyae B1 in polycyclic aromatic hydrocarbon degradation. O Cho KY Choi GJ Zylstra YS Kim SK Kim JH Lee HY Sohn GS Kwon YM Kim E Kim, Biochem Biophys Res Commun 2005 327 3 656 662 10.1016/j.bbrc.2004.12.060 15649397
13. Association of a common reductase with multiple aromatic terminal dioxygenases in Sphingomonas yanoikuyae strain B1. M Bae E Kim, J Microbiol 2000 38 40 43
14. Cloning, sequencing, and characterization of a multicomponent biphenyl dioxygenase system from Sphingomonas yanoikuyae B1: Abstract. E Moritz SM Ni' Chadhain E Kim GJ Zylstra, 104th General Meeting of the American Society for Microbiology, New Orleans, LA 2004
15. Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01. X Dong S Fushinobu E Fukuda T Terada S Nakamura K Shimizu H Nojiri T Omori H Shoun T Wakagi, J Bacteriol 2005 187 7 2483 2490 15774891 10.1128/JB.187.7.2483-2490.2005
16. Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1. Y Furusawa V Nagarajan M Tanokura E Masai M Fukuda T Senda, J Mol Biol 2004 342 3 1041 1052 10.1016/j.jmb.2004.07.062 15342255
17. Steady-state kinetic characterization and crystallization of a polychlorinated biphenyl-transforming dioxygenase. NY Imbeault JB Powlowski CL Colbert JT Bolin LD Eltis, J Biol Chem 2000 275 17 12430 12437 10.1074/jbc.275.17.12430 10777527
18. Pinpointing biphenyl dioxygenase residues that are crucial for substrate interaction. M Zielinski S Kahl HJ Hecht B Hofer, J Bacteriol 2003 185 23 6976 6980 14617661 10.1128/JB.185.23.6976-6980.2003
19. Engineering dioxygenases for efficient degradation of environmental pollutants. K Furukawa, Curr Opin Biotechnol 2000 11 3 244 249 10.1016/S0958-1669(00)00091-4 10851151
20. Biphenyl dioxygenases: functional versatilities and directed evolution. K Furukawa H Suenaga M Goto, J Bacteriol 2004 186 16 5189 5196 15292119 10.1128/JB.186.16.5189-5196.2004
21. Genetic construction of PCB degraders. V Brenner JJ Arensdorf DD Focht, Biodegradation 1994 5 3-4 359 377 10.1007/BF00696470 7765843
22. Aerobic degradation of polychlorinated biphenyls. DH Pieper, Appl Microbiol Biotechnol 2005 67 2 170 191 10.1007/s00253-004-1810-4 15614564
23. Rieske business: Structure-function of Rieske non-heme oxygenases. DJ Ferraro L Gakhar S Ramaswamy, Biochem Biophys Res Commun 2005 338 1 175 190 10.1016/j.bbrc.2005.08.222 16168954
24. Involvement of electrostatic interactions between the components of toluene dioxygenase from Pseudomonas putida F1. K Lee, J Microbiol Biotechnol 1998 8 4 416 421
25. A solution for the best rotation to relate two sets of vectors. W Kabsch, Acta Crystallogr A 1976 32 5 922 923 10.1107/S0567739476001873
26. Structure and increased thermostability of Rhodococcus sp. naphthalene 1,2-dioxygenase. L Gakhar ZA Malik CC Allen DA Lipscomb MJ Larkin S Ramaswamy, J Bacteriol 2005 187 21 7222 7231 16237006 10.1128/JB.187.21.7222-7231.2005
27. Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron. A Karlsson JV Parales RE Parales DT Gibson H Eklund S Ramaswamy, Science 2003 299 5609 1039 1042 10.1126/science.1078020 12586937
28. Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. B Kauppi K Lee E Carredano RE Parales DT Gibson H Eklund S Ramaswamy, Structure 1998 6 5 571 586 10.1016/S0969-2126(98)00059-8 9634695
29. Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase. H Nojiri Y Ashikawa H Noguchi JW Nam M Urata Z Fujimoto H Uchimura T Terada S Nakamura K Shimizu T Yoshida H Habe T Omori, J Mol Biol 2005 351 2 355 370 10.1016/j.jmb.2005.05.059 16005887
30. 2-Oxoquinoline 8-monooxygenase oxygenase component: active site modulation by Rieske-[2Fe-2S] center oxidation/reduction. BM Martins T Svetlitchnaia H Dobbek, Structure 2005 13 5 817 824 10.1016/j.str.2005.03.008 15893671
31. SCOP: a structural classification of proteins database for the investigation of sequences and structures. AG Murzin SE Brenner T Hubbard C Chothia, J Mol Biol 1995 247 4 536 540 10.1006/jmbi.1995.0159 7723011
32. Benzoate 1,2-dioxygenase from Pseudomonas putida: single turnover kinetics and regulation of a two-component Rieske dioxygenase. MD Wolfe DJ Altier A Stubna CV Popescu E Munck JD Lipscomb, Biochemistry 2002 41 30 9611 9626 10.1021/bi025912n 12135383
33. Hydrogen peroxide-coupled cis-diol formation catalyzed by naphthalene 1,2-dioxygenase. MD Wolfe JD Lipscomb, J Biol Chem 2003 278 2 829 835 10.1074/jbc.M209604200 12403773
34. Substrate binding to the mononuclear ferrous ion of the Rieske dioxygenase naphthalene 1,2-dioxygenase from Pseudomonas sp NCIB 9816-4. MD Wolfe J Parales K Lee DT Gibson JD Lipscomb, J Inorg Biochem 1999 74 1-4 339
35. Single turnover chemistry and regulation of O2 activation by the oxygenase component of naphthalene 1,2-dioxygenase. MD Wolfe JV Parales DT Gibson JD Lipscomb, J Biol Chem 2001 276 3 1945 1953 11056161
36. Modulation of substrate binding to naphthalene 1,2-dioxygenase by Rieske cluster reduction/oxidation. TC Yang MD Wolfe MB Neibergall Y Mekmouche JD Lipscomb BM Hoffman, J Am Chem Soc 2003 125 8 2034 2035 10.1021/ja028781m 12590516
37. Substrate binding to NO-ferro-naphthalene 1,2-dioxygenase studied by high-resolution Q-band pulsed 2H-ENDOR spectroscopy. TC Yang MD Wolfe MB Neibergall Y Mekmouche JD Lipscomb BM Hoffman, J Am Chem Soc 2003 125 23 7056 7066 10.1021/ja0214126 12783560
38. Structural and mechanistic studies of Rieske dioxygenases. A Karlsson, Department of Molecular Biology. Uppsala, Sweden, The Swedish University of Agricultural Sciences 2002
39. NO binding to naphthalene dioxygenase. A Karlsson JV Parales RE Parales DT Gibson H Eklund S Ramaswamy, J Biol Inorg Chem 2005 15942729
40. Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding. E Carredano A Karlsson B Kauppi D Choudhury RE Parales JV Parales K Lee DT Gibson H Eklund S Ramaswamy, J Mol Biol 2000 296 2 701 712 10.1006/jmbi.1999.3462 10669618
41. Structure-function studies of iron sulfur enzyme systems. R Friemann, Department of Molecular Biology. Uppsala, Sweden, The Swedish University of Agricultural Sciences 2005
42. Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase. R Friemann MM Ivkovic-Jensen DJ Lessner CL Yu DT Gibson RE Parales H Eklund S Ramaswamy, J Mol Biol 2005 348 5 1139 1151 10.1016/j.jmb.2005.03.052 15854650
43. The role of active-site residues in naphthalene dioxygenase. RE Parales, J Ind Microbiol Biotechnol 2003 30 5 271 278 10.1007/s10295-003-0043-3 12695887
44. Absolute stereochemistry of the (+)-cis-1,2-dihydroxy-3-methylcyclohexa- 3,5-diene produced from toluene by Pseudomonas putida. H Ziffer DM Jerina DT Gibson VM Kobal, J Am Chem Soc 1973 95 12 4048 4049 10.1021/ja00793a036 4710064
45. Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase. DJ Ferraro AL Okerlund JC Mowers S Ramaswamy, J Bacteriol 2006 188 19 6986 6994 16980501 10.1128/JB.00707-06
46. A cluster exposed: structure of the Rieske ferredoxin from biphenyl dioxygenase and the redox properties of Rieske Fe-S proteins. CL Colbert MM Couture LD Eltis JT Bolin, Structure 2000 8 12 1267 1278 10.1016/S0969-2126(00) 00536-0 11188691
47. Structure of a water soluble fragment of the 'Rieske' iron-sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5 Å resolution. S Iwata M Saynovits TA Link H Michel, Structure 1996 4 5 567 579 10.1016/S0969-2126(96)00062-7 8736555
48. Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system. JW Nam H Noguchi Z Fujimoto H Mizuno Y Ashikawa M Abo S Fushinobu N Kobashi T Wakagi K Iwata T Yoshida H Habe H Yamane T Omori H Nojiri, Proteins 2005 58 4 779 789 10.1002/prot.20374 15645447
49. Solution structure of T4moC, the Rieske ferredoxin component of the toluene 4-monooxygenase complex. L Skjeldal FC Peterson JF Doreleijers LA Moe JD Pikus WM Westler JL Markley BF Volkman BG Fox, J Biol Inorg Chem 2004 9 8 945 953 10.1007/s00775-004-0594-4 15452777
50. Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme. RE Parales K Lee SM Resnick H Jiang DJ Lessner DT Gibson, J Bacteriol 2000 182 6 1641 1649 10692370 10.1128/JB.182.6.1641-1649.2000
51. Bacterial oxidation of chemical carcinogens: formation of polycyclic aromatic acids from benz[a]anthracene. WR Mahaffey DT Gibson CE Cerniglia, Appl Environ Microbiol 1988 54 10 2415 2423 2462407
52. The finer things in X-ray diffraction data collection. JW Pflugrath, Acta Crystallogr D Biol Crystallogr 1999 55 Pt 10 1718 1725 10.1107/ S090744499900935X 10531521
53. AMoRe: an automated package for molecular replacement. J Navaza, Acta Crystallogr A 1994 50 157 163 10.1107/S0108767393007597
54. Improved methods for building protein models in electron density maps and the location of errors in these models. TA Jones JY Zou SW Cowan Kjeldgaard, Acta Crystallogr A 1991 47 Pt 2 110 119 10.1107/S0108767390010224 2025413
55. Coot: model-building tools for molecular graphics. P Emsley K Cowtan, Acta Crystallogr D Biol Crystallogr 2004 60 Pt 12 Pt 1 2126 2132 10.1107/S0907444904019158 15572765
56. Refinement of macromolecular structures by the maximum- likelihood method. GN Murshudov AA Vagin EJ Dodson, Acta Crystallogr D Biol Crystallogr 1997 53 240 255 10.1107/S0907444996012255 15299926
57. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. A Perrakis TK Sixma KS Wilson VS Lamzin, Acta Crystallogr D Biol Crystallogr 1997 53 Pt 4 448 455 10.1107/S0907444997005696 15299911
58. Automated refinement of protein models. VS Lamzin KS Wilson, Acta Crystallogr D Biol Crystallogr 1993 49 Pt 1 129 147 10.1107/S0907444992008886 15299554
59. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994 50 Pt 5 760 763 15299374
60. A visual protein crystallographic software system for X11/XView. DE McRee, J Mol Graphics 1992 10 44 46 10.1016/0263-7855(92)80022-6
61. Solvent content of protein crystals. BW Matthews, J Mol Biol 1968 33 491 497 10.1016/0022-2836(68)90205-2 5700707
62. SYBYL. Version 7.1. St. Louis, MO, Tripos, Inc.
63. Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. O Poirot E O'Toole C Notredame, Nucleic Acids Res 2003 31 13 3503 3506 12824354 10.1093/nar/gkg522
64. Indonesia. D Madsen P Johansson GJ Kleywegt, Version 1.4. Uppsala, Sweden, Uppsala Software Factory 2002 An integrated sequence analysis program
65. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 9254694 10.1093/nar/25.17.3389
66. The PyMOL Molecular Graphics System. WL DeLano, Version 0.98. San Carlos, CA, USA, DeLano Scientific 2000
67. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. AC Wallace RA Laskowski JM Thornton, Protein Eng 1995 8 2 127 134 10.1093/protein/8.2.127 7630882