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Title: Structural Investigations of the Ferredoxin and Terminal Oxygenase Components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1

Abstract

The initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism Sphingobium yanoikuyae strain B1 (B1), previously known as Sphingomonas yanoikuyae strain B1 and Beijerinckia sp. strain B1, is performed by a set of multiple terminal Rieske non-heme iron oxygenases. These enzymes share a single electron donor system consisting of a reductase and a ferredoxin (BPDO-F{sub B1}). One of the terminal Rieske oxygenases, biphenyl 2,3-dioxygenase (BPDO-O{sub B1}), is responsible for B1's ability to dihydroxylate large aromatic compounds, such as chrysene and benzo(a)pyrene. Results: In this study, crystal structures of BPDO-O{sub B1} in both native and biphenyl bound forms are described. Sequence and structural comparisons to other Rieske oxygenases show this enzyme to be most similar, with 43.5 % sequence identity, to naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4. While structurally similar to naphthalene 1,2-dioxygenase, the active site entrance is significantly larger than the entrance for naphthalene 1,2-dioxygenase. Differences in active site residues also allow the binding of large aromatic substrates. There are no major structural changes observed upon binding of the substrate. BPDO-F{sub B1} has large sequence identity to other bacterial Rieske ferredoxins whose structures are known and demonstrates a high structural homology; however, differencesmore » in side chain composition and conformation around the Rieske cluster binding site are noted. Conclusion: This is the first structure of a Rieske oxygenase that oxidizes substrates with five aromatic rings to be reported. This ability to catalyze the oxidation of larger substrates is a result of both a larger entrance to the active site as well as the ability of the active site to accommodate larger substrates. While the biphenyl ferredoxin is structurally similar to other Rieske ferredoxins, there are distinct changes in the amino acids near the iron-sulfur cluster. Because this ferredoxin is used by multiple oxygenases present in the B1 organism, this ferredoxin-oxygenase system provides the structural platform to dissect the balance between promiscuity and selectivity in protein-protein electron transport systems.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
930655
Report Number(s):
BNL-81128-2008-JA
TRN: US200901%%166
DOE Contract Number:  
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: BMC Structural Biology; Journal Volume: 7
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; AMINO ACIDS; BINDING ENERGY; BIPHENYL; CRYSTAL STRUCTURE; FERREDOXIN; NAPHTHALENE; OXYGENASES; SUBSTRATES; national synchrotron light source

Citation Formats

Ferraro,D., Brown, E., Yu, C., Parales, R., Gibson, D., and Ramaswamy, S. Structural Investigations of the Ferredoxin and Terminal Oxygenase Components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1. United States: N. p., 2007. Web. doi:10.1186/1472-6807-7-10.
Ferraro,D., Brown, E., Yu, C., Parales, R., Gibson, D., & Ramaswamy, S. Structural Investigations of the Ferredoxin and Terminal Oxygenase Components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1. United States. doi:10.1186/1472-6807-7-10.
Ferraro,D., Brown, E., Yu, C., Parales, R., Gibson, D., and Ramaswamy, S. Mon . "Structural Investigations of the Ferredoxin and Terminal Oxygenase Components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1". United States. doi:10.1186/1472-6807-7-10.
@article{osti_930655,
title = {Structural Investigations of the Ferredoxin and Terminal Oxygenase Components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1},
author = {Ferraro,D. and Brown, E. and Yu, C. and Parales, R. and Gibson, D. and Ramaswamy, S.},
abstractNote = {The initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism Sphingobium yanoikuyae strain B1 (B1), previously known as Sphingomonas yanoikuyae strain B1 and Beijerinckia sp. strain B1, is performed by a set of multiple terminal Rieske non-heme iron oxygenases. These enzymes share a single electron donor system consisting of a reductase and a ferredoxin (BPDO-F{sub B1}). One of the terminal Rieske oxygenases, biphenyl 2,3-dioxygenase (BPDO-O{sub B1}), is responsible for B1's ability to dihydroxylate large aromatic compounds, such as chrysene and benzo(a)pyrene. Results: In this study, crystal structures of BPDO-O{sub B1} in both native and biphenyl bound forms are described. Sequence and structural comparisons to other Rieske oxygenases show this enzyme to be most similar, with 43.5 % sequence identity, to naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4. While structurally similar to naphthalene 1,2-dioxygenase, the active site entrance is significantly larger than the entrance for naphthalene 1,2-dioxygenase. Differences in active site residues also allow the binding of large aromatic substrates. There are no major structural changes observed upon binding of the substrate. BPDO-F{sub B1} has large sequence identity to other bacterial Rieske ferredoxins whose structures are known and demonstrates a high structural homology; however, differences in side chain composition and conformation around the Rieske cluster binding site are noted. Conclusion: This is the first structure of a Rieske oxygenase that oxidizes substrates with five aromatic rings to be reported. This ability to catalyze the oxidation of larger substrates is a result of both a larger entrance to the active site as well as the ability of the active site to accommodate larger substrates. While the biphenyl ferredoxin is structurally similar to other Rieske ferredoxins, there are distinct changes in the amino acids near the iron-sulfur cluster. Because this ferredoxin is used by multiple oxygenases present in the B1 organism, this ferredoxin-oxygenase system provides the structural platform to dissect the balance between promiscuity and selectivity in protein-protein electron transport systems.},
doi = {10.1186/1472-6807-7-10},
journal = {BMC Structural Biology},
number = ,
volume = 7,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}