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Please use this identifier to cite or link to this item: http://repository.iitr.ac.in/handle/123456789/26947
Title: Structural Characterization of Pandoraea pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes
Authors: Colbert C.L.
Agar N.Y.R.
Kumar, Pravindra R.Manish
Chakko M.N.
Sinha S.C.
Powlowski J.B.
Eltis L.D.
Bolin J.T.
Published in: PLoS ONE
Abstract: The oxidative degradation of biphenyl and polychlorinated biphenyls (PCBs) is initiated in Pandoraea pnomenusa B-356 by biphenyl dioxygenase (BPDOB356). BPDOB356, a heterohexameric (αβ)3 Rieske oxygenase (RO), catalyzes the insertion of dioxygen with stereo- and regioselectivity at the 2,3-carbons of biphenyl, and can transform a broad spectrum of PCB congeners. Here we present the X-ray crystal structures of BPDOB356 with and without its substrate biphenyl 1.6-Å resolution for both structures. In both cases, the Fe(II) has five ligands in a square pyramidal configuration: H233 Nε2, H239 Nε2, D386 Oδ1 and Oδ2, and a single water molecule. Analysis of the active sites of BPDOB356 and related ROs revealed structural features that likely contribute to the superior PCB-degrading ability of certain BPDOs. First, the active site cavity readily accommodates biphenyl with minimal conformational rearrangement. Second, M231 was predicted to sterically interfere with binding of some PCBs, and substitution of this residue yielded variants that transform 2,2′-dichlorobiphenyl more effectively. Third, in addition to the volume and shape of the active site, residues at the active site entrance also apparently influence substrate preference. Finally, comparison of the conformation of the active site entrance loop among ROs provides a basis for a structure-based classification consistent with a phylogeny derived from amino acid sequence alignments. © 2013 Colbert et al.
Citation: PLoS ONE, 8(1)
URI: https://doi.org/10.1371/journal.pone.0052550
http://repository.iitr.ac.in/handle/123456789/26947
Issue Date: 2013
Keywords: biphenyl
biphenyl dioxygenase
dichlorobiphenyl
dioxygenase
ferrous ion
polychlorinated biphenyl
unclassified drug
water
article
bacterium
beta chain
binding affinity
binding site
conformational transition
controlled study
crystal structure
crystallization
enzyme active site
enzyme binding
enzyme conformation
mutagenesis
nucleotide sequence
Pandoraea pnomenusa
phylogeny
steady state
structure analysis
X ray crystallography
Biphenyl Compounds
Burkholderiaceae
Catalytic Domain
Crystallography, X-Ray
Dioxygenases
Models, Molecular
Mutagenesis
Phylogeny
Polychlorinated Biphenyls
Protein Conformation
Protein Subunits
Substrate Specificity
Pandoraea pnomenusa
ISSN: 19326203
Author Scopus IDs: 7004670833
8966079700
55064809000
55543777300
57202564009
7004324227
7003863696
57197844041
Author Affiliations: Colbert, C.L., Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, United States, Department of Biological Sciences and Center for Cancer Research, Purdue University, West Lafayette, IN, United States
Agar, N.Y.R., Department of Neurosurgery and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States, Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada
Kumar, P., Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India, Department of Biological Sciences and Center for Cancer Research, Purdue University, West Lafayette, IN, United States
Chakko, M.N., Department of Diagnostic Radiology, Providence Hospital and Medical Centers, Southfield, MI, United States, Department of Biological Sciences and Center for Cancer Research, Purdue University, West Lafayette, IN, United States
Sinha, S.C., Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, United States
Powlowski, J.B., Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada
Eltis, L.D., Departments of Microbiology and Biochemistry, Life Sciences Institute, University of British Columbia, Vancouver, Canada
Bolin, J.T., Department of Biological Sciences and Center for Cancer Research, Purdue University, West Lafayette, IN, United States
Funding Details: National Science Foundation, NSF: 0814442; National Institute of General Medical Sciences, NIGMS: P30GM103332, P41GM103543, R01GM052381, T32GM008296; National Center for Research Resources, NCRR: P20RR015566, P41RR007707
Corresponding Author: Colbert, C. L.; Department of Chemistry and Biochemistry, , Fargo, ND, United States; email: christopher.colbert@ndsu.edu
Appears in Collections:Journal Publications [BT]

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