+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

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



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



Journal of Molecular Biology 255(5): 735-752



The crystal structure of an enzyme having polychlorinated-biphenyl degrading activity the BphC enzyme from Pseudomonas sp. strain KKS102, has been solved as a free form at 1.8 ANG resolution. This is the first three-dimensional structure among the extradiol-type dioxygenases. Based on 34,387 reflections (10.0 to 1.8 ANG , completeness 87.8%), a current R-factor of 20.4% (with a free R-factor of 24.3%) was obtained with a model obeying standard geometry within 0.011 ANG in bond lengths and 1.91 degree in bond angles. The BphC enzyme is a homo-octamer and each subunit is composed of two domains: Domain 1 (N-terminal part) and Domain 2 (C-terminal part). Each domain contains two repetitions of a novel folding motif (the "beta-alpha-beta-beta-beta" motif) each consisting of ca 55 amino acid residues. A single Fe ion in the active site coordinates the side-chains of three amino acid residues (His145, His209 and Glu260) and two solvent molecules. The coordination geometry is that of a square pyramid. In addition to the free form of the BphC enzyme, we have solved two three-dimensional structures of the BphC enzyme complexed with its substrates, 2,3-dihydroxybiphenyl (2,3-DHBP) or 3-methylcatechol (3-MCT). These substrates were found intact in the active site probably because of the oxidation of the Fe ion into ferric form (as judged by EPR spectra) in the present crystals. In both of the two substrate complexes, the two hydroxyl groups of the substrate, together with the three enzymatic side-chain ligands, were found to form a penta-coordinated system around the Fe ion roughly arranged in a trigonal bipyramidal configuration. The active site structures appear to be essentially consistent with the reaction mechanism proposed so far.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 009646008

Download citation: RISBibTeXText

PMID: 8636975

DOI: 10.1006/jmbi.1996.0060


Related references

Three-dimensional structure of an extradiol-type catechol ring cleavage dioxygenase BphC derived from Pseudomonas sp strain KKS102 Structural features pertinent to substrate specificity and reaction mechanisms. Ishimura, Y , Shimada, H , Suematsu, M Keio University Symposia for Life Science and Medicine, Vol 1; Oxygen homeostasis and its dynamics 276-281, 1998

Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase. Journal of Inorganic Biochemistry 83(4): 269-279, 2001

A Novel Bacterium That Degrades Aroclor-1254 and Its bphC Gene Encodes an Extradiol Aromatic Ring Cleavage Dioxygenase EARCD. Water, Air & Soil Pollution 224(6): 1587, 2013

Three-dimensional Structure of 2,3-Dihydroxybiphenyl Dioxygenase from Pseudomonas sp Strain KKS102 Having Polychlorinated Biphenyl -Degrading Activity. Proceedings of the Japan Academy Series B Physical & Biological Sciences 71(1): 32-35, 1995

Crystallization and preliminary X-ray analysis of the Rieske-type [2Fe-2S] ferredoxin component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications 62(Pt 6): 590-592, 2006

Extradiol cleavage of two-ring structures of biphenyl and indole oxidation by biphenyl dioxygenase in Commamonas acidovorans. Journal of Microbiology & Biotechnology 8(3): 264-269, 1998

Microbial metabolism of quinoline and related compounds. XIV. Purification and properties of 1H-3-hydroxy-4-oxoquinoline oxygenase, a new extradiol cleavage enzyme from Pseudomonas putida strain 33/1. Biological Chemistry Hoppe-Seyler 373(6): 343-349, 1992

Cloning of a gene encoding hydroxyquinol 1,2-dioxygenase that catalyzes both intradiol and extradiol ring cleavage of catechol. Bioscience Biotechnology and Biochemistry 63(5): 859-865, 1999

2-aminophenol 1,6-dioxygenase: a novel aromatic ring cleavage enzyme purified from Pseudomonas pseudoalcaligenes JS45. Journal of Bacteriology 178(21): 6227-6232, 1996

Crystallization and preliminary crystallographic analysis of a 2,3-dihydroxybiphenyl dioxygenase from Pseudomonas sp. strain KKS102 having polychlorinated biphenyl (PCB)-degrading activity. Proteins 22(3): 284-286, 1995

Substrate binding mechanism of a type I extradiol dioxygenase. Journal of Biological Chemistry 285(45): 34643-34652, 2010

Quantitative structure-activity relationship for the cleavage of C3/C4-substituted catechols by a prototypal extradiol catechol dioxygenase with broad substrate specificity. Journal of Biochemistry 135(6): 721-730, 2004