Dioxygenase from Aspergillus fumigatus MC8: molecular modelling and in silico studies on enzyme–substrate interactions

References

• Burton , S.G. 2003 . Oxidizing enzymes as biocatalysts . Trends in Biotech. , 21 ( 12 ) : 543 – 549 .
   Google Scholar
• Li , Z. , van Beilen , J.B. , Duetz , A.W. , Schmid , A. , de Raadt , A. , Griengl , H. and Witholt , B. 2002 . Oxidative biotransformations using oxygenases . Curr. Opin. Chem. Biol. , 6 : 136 – 144 .
   Google Scholar
• Wackett , L.P. 2002 . Mechanism and applications of Rieske non-heam iron dioxygenases . Enzyme Microb. Technol. , 31 : 577 – 587 .
   Google Scholar
• Holland , H.L. 1992 . Organic Synthesis with Oxidative Enzymes 5 – 40 . New York : VCH Publishers Inc., .
   Google Scholar
• Broderick , J.B. 1999 . Catechol dioxygenases . Essays Biochem. , 34 : 173 – 189 .
   PubMedGoogle Scholar
• Harayama , S. , Kok , M. and Neidle , E.L. 1992 . Functional and evolutionary relationships among diverse oxygenases . Annu. Rev. Microbiol. , 46 : 565 – 601 .
   PubMed Web of Science ®Google Scholar
• Noda , Y. , Nishikawa , S. , Shiozuka , K.I. , Kadokura , H. , Nakajima , H. , Yoda , K. , Katayama , Y. , Morohoshi , N. , Haraguchi , T. and Yamasaki , M. 1990 . Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis . J. Bacteriol. , 172 : 2704 – 2709 .
   PubMedGoogle Scholar
• Roper , D.I. and Cooper , R.A. 1990 . Subcloning and nucleotide sequence of the 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase gene from Escherichia coli C . FEBS Lett. , 275 : 53 – 57 .
   Google Scholar
• Kabisch , M. and Fortnagel , P. 1990 . Nucleotide sequence of metapyrocatechase I (catechol 2,3-oxygenase I) gene mpcI from Alcaligenes eutrophus JMP222 . Nucl. Acid. Res. , 18 : 3405 – 3406 .
   PubMed Web of Science ®Google Scholar
• Han , S. , Eltis , L.D. , Timmis , K.N. , Muchmore , S.W. and Bolin , J.T. 1995 . Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCBFIG degrading Pseudomonad . Science , 270 : 976 – 980 .
   PubMed Web of Science ®Google Scholar
• Lee , K. , Kauppi , B. , Parales , R.E. , Gibson , D.T. and Ramaswany , S. 1997 . Purification and crystallization of the oxygenase component of naphthalene dioxygenase in native and selenomethionine-derivatized forms . Biochem. Biophys. Res. Commun. , 241 : 553 – 557 .
   Google Scholar
• Gowthaman , U. , Jayakanthan , M. and Sundar , D. 2008 . Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: Computational screening of inhibitors to HIV-1 entry . BMC Bioinform , 9 ( Suppl. 12 ) : S14
   PubMedGoogle Scholar
• Roopesh , K. , Guyot , S. , Sabu , A. , Isabelle , P.G. , Roussos , S. and Augur , C. 2010 . Biotransformation of procyanidins by a purified fungal dioxygenase: Identification and characterization of the products using mass spectrometry . Proc. Biochem. , 45 : 904 – 913 .
   Google Scholar
• Thompson , J.D. , Higgins , D.J. and Gibson , T.J. 1994 . CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice . Nucl. Acid. Res. , 22 : 4673 – 4680 .
   PubMed Web of Science ®Google Scholar
• Altschul , S.F. , Madden , T.L. , Schaffer , A.A. , Zhang , J. , Zhang , Z. , Miller , W. and Lipman , D.J. 1997 . Gapped BLAST and PSI-BLAST: A new generation of protein database search programs . Nucl. Acid. Res. , 25 : 3389 – 3402 .
   PubMed Web of Science ®Google Scholar
• Kelley , L.A. and Sternberg , M.J.E. 2009 . Protein structure prediction on the web: A case study using the Phyre server . Nat. protoc. , 4 : 363 – 371 .
   PubMed Web of Science ®Google Scholar
• Sayle , R.A. and Milner-White , E.J. 1995 . RASMOL: Biomoleculer graphics for all . Trends Biochem. Sci. , 20 : 374 – 376 .
   PubMed Web of Science ®Google Scholar
• Halgren , T.A. , Murphy , R.B. , Friesner , R.A. , Beard , H.S. , Frye , L.L. , Pollard , W.T. and Banks , J.L. 2004 . Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening . J. Med. Chem. , 47 : 1750 – 1759 .
   PubMed Web of Science ®Google Scholar
• Friesner , R.A. , Banks , J.L. , Murphy , R.B. , Halgren , T.A. , Klicic , J.J. , Mainz , D.T. , Repasky , M.P. , Knoll , E.H. , Shelley , M. , Perry , J.K. , Shaw , D.E. , Francis , P. and Shenkin , P.S. 2004 . Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy . J. Med. Chem. , 47 : 1739 – 1749 .
   PubMed Web of Science ®Google Scholar
• Jorgensen , W.L. , Maxwell , D.S. and Tirado-Rives , J. 1996 . Development and testing of the OPLS all-atom force field on conformational energetics of organic liquids . J. Am. Chem. Soc. , 118 : 11225 – 11236 .
   Web of Science ®Google Scholar
• Friesner , R.A. , Murphy , R.B. , Repasky , M.P. , Frye , L.L. , Greenwood , J.R. , Halgren , T.A. , Sanschagrin , P.C. and Mainz , D.T. 2006 . Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes . J. Med. Chem. , 49 : 6177 – 6196 .
   PubMed Web of Science ®Google Scholar
• Ferraroni , M. , Kolomytseva , P.M. , Solyanikova , P.I. , Scozzafava1 , A. , Golovleva , A.L. and Briganti , F. 2006 . Crystal structure of 3-chlorocatechol 1,2-dioxygenase key enzyme of a new modified ortho-pathway from the gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol . J. Mol. Biol. , 360 : 788 – 799 .
   Google Scholar
• Vetting , M.W. and Ohlendorf , D.H. 2000 . The 1.8 Å crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker . Struct. Fold. Des. , 8 : 429 – 440 .
   Google Scholar
• Sherman , B. , Day , T. , Jacobson , M.P. , Friesner , R.A. and Farid , R.A. 2006 . Novel procedure for modeling ligand/receptor induced fit effects . J. Med. Chem. , 49 : 534 – 553 .
   PubMed Web of Science ®Google Scholar
• Sheridan , R.P. , Miller , M.D. , Underwood , D.J. and Kearsley , S.K. 1996 . Chemical similarity using geometric atom pair descriptors . J. Chem. Inform. Comput. Sci. , 36 : 128 – 136 .
   Google Scholar
• Eldridge , M.D. , Murray , C.W. , Auton , T.R. , Paolini , G.V. and Mee , R.P. 1997 . Empirical scoring functions: The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes . J. Comput. Aided Mol. Des. , 11 : 425 – 445 .
   PubMed Web of Science ®Google Scholar
• Nierman , W.C. , Pain , A. , Anderson , M.J. , Wortman , J.R. , Kim , H.S. , Arroyo , J. , Berriman , M. , Abe , K. , Archer , D.B. , Bermejo , C. , Bennett , J. , Bowyer , P. , Chen , D. , Collins , M. , Coulsen , R. , Davies , R. , Dyer , P.S. , Farman , M. , Fedorova , N. , Fedorova , N. , Feldblyum , T.V. , Fischer , R. , Fosker , N. , Fraser , A. , García , J.L. , García , M.J. , Goble , A. , Goldman , G.H. , Gomi , K. , Griffith-Jones , S. , Gwilliam , R. , Haas , B. , Haas , H. , Harris , D. , Horiuchi , H. , Huang , J. , Humphray , S. , Jiménez , J. , Keller , N. , Khouri , H. , Kitamoto , K. , Kobayashi , T. , Konzack , S. , Kulkarni , R. , Kumagai , T. , Lafon , A. , Latgé , J.P. , Li , W. , Lord , A. , Lu , C. , Majoros , W.H. , May , G.S. , Miller , B.L. , Mohamoud , Y. , Molina , M. , Monod , M. , Mouyna , I. , Mulligan , S. , Murphy , L. , O'Neil , S. , Paulsen , I. , Peñalva , M.A. , Pertea , M. , Price , C. , Pritchard , B.L. , Quail , M.A. , Rabbinowitsch , E. , Rawlins , N. , Rajandream , M.A. , Reichard , U. , Renauld , H. , Robson , G.D. , Rodriguez de Córdoba , S. , Rodríguez-Peña , J.M. , Ronning , C.M. , Rutter , S. , Salzberg , S.L. , Sanchez , M. , Sánchez-Ferrero , J.C. , Saunders , D. , Seeger , K. , Squares , R. , Squares , S. , Takeuchi , M. , Tekaia , F. , Turner , G. , Vazquez de Aldana , C.R. , Weidman , J. , White , O. , Woodward , J. , Yu , J.H. , Fraser , C. , Galagan , J.E. , Asai , K. , Machida , M. , Hall , N. , Barrell , B. and Denning , D.W. 2005 . Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus . Nature , 438 : 1151 – 1156 .
   PubMed Web of Science ®Google Scholar
• Ohlendorf , D.H. , Lipscomb , J.D. and Weber , P.C. 1988 . Structure and assembly of protocatechuate 3,4-dioxygenase . Nature , 336 : 403 – 405 .
   Google Scholar
• Vetting , M.W. , D'Argenio , D.A. , Ornston , L.N. and Ohlendorf , D.H. 2000 . Structure of Acinetobacter strain ADP1 protocatechuate 3,4-dioxygenase at 2.2 Å resolution: Implications for the mechanism of an intradiol dioxygenase . Biochemistry , 39 : 7943 – 7955 .
   PubMed Web of Science ®Google Scholar
• Orville , A.M. , Lipscomb , J.D. and Ohlendorf , D.H. 1997 . Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: Endogenous Fe3+ ligand displacement in response to substrate binding . Biochemistry , 36 : 10052 – 10066 .
   PubMed Web of Science ®Google Scholar
• Elgren , T.E. , Orville , A.M. , Kelly , K.A. , Lipscomb , J.D. , Ohlendorf , D.H. and Que , L. Jr . 1997 . Crystal structure and resonance Raman studies of protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate . Biochemistry , 36 : 11504 – 11513 .
   PubMed Web of Science ®Google Scholar