Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase.

Oxidative biodegradation of aromatic compounds by bacteria usually begins with hydroxylation of the aromatic ring by multi-component dioxygenases like benzene dioxygenase, biphenyl dioxygenase, and others. These enzymes are composed of ferredoxin reductase, ferredoxin, and terminal oxygenase. Reducing equivalents that originate from NADH are transferred from ferredoxin reductase to ferredoxin and, in turn, to the terminal oxygenase, thus resulting in the activation of a dioxygen. BphA4 is the ferredoxin reductase component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102. The amino acid sequence of BphA4 exhibits significant homology with the putidaredoxin reductase of the cytochrome P450cam system in Pseudomonas putida, as well as with various other oxygenase-coupled NADH-dependent ferredoxin reductases (ONFRs) of bacteria. To date, no structural information has been provided for the ferredoxin reductase component of the dioxygenase systems. In order to provide a structural basis for discussing the mechanism of electron transport between ferredoxin reductase and ferredoxin, crystal structures of BphA4 and its NADH complex were solved. The three-dimensional structure of BphA4 is different from those of ferredoxin reductases whose structures have already been determined, but adopts essentially the same fold as the enzymes of the glutathione reductase (GR) family. Also the three-dimensional structure of the first two domains of BphA4 adopts a fold similar to that of adrenodoxin reductase (AdR) in the mitochondrial cytochrome P450 system. Comparing the amino acid sequence with what is known of the three-dimensional structure of BphA4 strongly suggests that the other ONFRs have secondary structural features that are similar to that of BphA4. This analysis of the crystal structures of BphA4 suggests that Lys53 and Glu159 seem to be involved in the hydride transfer from NADH to FAD. Since the amino acid residues around the active site, some of which seem to be important to electron transport, are highly conserved among ONFRs, it is likely that the mechanism of electron transport of BphA4 is quite applicable to other ONFRs.

[1]  Ruedi Aebersold,et al.  Molecular characterization of mitochondrial apoptosis-inducing factor , 1999, Nature.

[2]  I. Schlichting,et al.  The Structure of Trypanosoma cruzitrypanothione Reductase in the Oxidized and NADPH Reduced State , 1994, Proteins.

[3]  G. Schulz,et al.  Structure of glutathione reductase from escherichia coli at 1.86 Å resolution: Comparison with the enzyme from human erythrocytes , 1994, Protein science : a publication of the Protein Society.

[4]  P. Karplus,et al.  A productive NADP+ binding mode of ferredoxin–NADP + reductase revealed by protein engineering and crystallographic studies , 1999, Nature Structural Biology.

[5]  G. Schulz,et al.  The catalytic mechanism of glutathione reductase as derived from x-ray diffraction analyses of reaction intermediates. , 1983, The Journal of biological chemistry.

[6]  R. Cammack,et al.  The electron-transport proteins of hydroxylating bacterial dioxygenases. , 1992, Annual review of microbiology.

[7]  J. Kuriyan,et al.  Convergent evolution of similar function in two structurally divergent enzymes , 1991, Nature.

[8]  G. Vriend,et al.  X-ray structure of lipoamide dehydrogenase from Azotobacter vinelandii determined by a combination of molecular and isomorphous replacement techniques. , 1989, Journal of molecular biology.

[9]  J. Fontecilla-Camps,et al.  X-ray structure of the ferredoxin:NADP+ reductase from the cyanobacterium Anabaena PCC 7119 at 1.8 A resolution, and crystallographic studies of NADP+ binding at 2.25 A resolution. , 1996, Journal of molecular biology.

[10]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[11]  W. Kabsch,et al.  Structure of the detoxification catalyst mercuric ion reductase from Bacillus sp. strain RC607 , 1991, Nature.

[12]  C. C. Correll,et al.  Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe-2S]. , 1992, Science.

[13]  G. Vriend,et al.  Rubredoxin reductase of Pseudomonas oleovorans. Structural relationship to other flavoprotein oxidoreductases based on one NAD and two FAD fingerprints. , 1990, Journal of molecular biology.

[14]  M. Fukuda,et al.  Identification of the bphA4 gene encoding ferredoxin reductase involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102 , 1994, Journal of bacteriology.

[15]  P. Karplus,et al.  Substrate binding and catalysis by glutathione reductase as derived from refined enzyme: substrate crystal structures at 2 A resolution. , 1994, Journal of molecular biology.

[16]  E A Merritt,et al.  Raster3D Version 2.0. A program for photorealistic molecular graphics. , 1994, Acta crystallographica. Section D, Biological crystallography.

[17]  S. Harayama,et al.  Functional and evolutionary relationships among diverse oxygenases. , 1992, Annual review of microbiology.

[18]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[19]  K. Inaka,et al.  Crystal structure of NADH-cytochrome b5 reductase from pig liver at 2.4 A resolution. , 1995, Biochemistry.

[20]  M. Oishi,et al.  Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenyl to benzoic acid in the polychlorinated biphenyl-degrading soil bacterium Pseudomonas sp. strain KKS102 , 1989, Journal of bacteriology.

[21]  V. Luzzati,et al.  Traitement statistique des erreurs dans la determination des structures cristallines , 1952 .

[22]  N. Sakabe.  X-ray diffraction data collection system for modern protein crystallography with a Weissenberg camera and an imaging plate using synchrotron radiation , 1991 .

[23]  G. Schulz,et al.  The structure of the flavoenzyme glutathione reductase , 1978, Nature.

[24]  B. Masters,et al.  Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN- and FAD-containing enzymes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[25]  H. Eklund,et al.  The three-dimensional structure of flavodoxin reductase from Escherichia coli at 1.7 A resolution. , 1997, Journal of molecular biology.

[26]  J. Kingma,et al.  The Pseudomonas oleovorans alkBAC operon encodes two structurally related rubredoxins and an aldehyde dehydrogenase. , 1989, The Journal of biological chemistry.

[27]  V S Lamzin,et al.  Automated refinement of protein models. , 1993, Acta crystallographica. Section D, Biological crystallography.

[28]  Y. Yasukochi,et al.  Nucleotide sequence and functional analysis of the meta-cleavage pathway involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102 , 1994, Journal of bacteriology.

[29]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[30]  G. Schulz,et al.  The structure of adrenodoxin reductase of mitochondrial P450 systems: electron transfer for steroid biosynthesis. , 1999, Journal of molecular biology.

[31]  R. Schirmer,et al.  Role of active site tyrosine residues in catalysis by human glutathione reductase. , 1998, Biochemistry.

[32]  Axel T. Brunger,et al.  Model bias in macromolecular crystal structures , 1992 .

[33]  A. Brunger.  Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[34]  J. V. Van Beeumen,et al.  The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium. , 1994, Science.

[35]  P. Karplus,et al.  Atomic structure of ferredoxin-NADP+ reductase: prototype for a structurally novel flavoenzyme family. , 1991, Science.

[36]  M. Haniu,et al.  The amino acid sequence of putidaredoxin, an iron-sulfur protein from Pseudomonas putida. , 1974, The Journal of biological chemistry.

[37]  G. N. Ramachandran,et al.  Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.

[38]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[39]  G. Schneider,et al.  Crystal structure of the FAD-containing fragment of corn nitrate reductase at 2.5 A resolution: relationship to other flavoprotein reductases. , 1994, Structure.

[40]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[41]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[42]  C. Betzel,et al.  The refined crystal structure of Pseudomonas putida lipoamide dehydrogenase complexed with NAD+ at 2.45 Å resolution , 1992, Proteins.

[43]  G. Schulz,et al.  Anatomy of an engineered NAD‐binding site , 1994, Protein science : a publication of the Protein Society.

[44]  Y. Yasukochi,et al.  Identification of the bphA and bphB genes of Pseudomonas sp. strains KKS102 involved in degradation of biphenyl and polychlorinated biphenyls. , 1994, Biochemical and biophysical research communications.