Literature DB >> 32094179

Evaluation of a concerted vs. sequential oxygen activation mechanism in α-ketoglutarate-dependent nonheme ferrous enzymes.

Serra Goudarzi1, Shyam R Iyer1, Jeffrey T Babicz1, James J Yan1,2, Günther H J Peters3, Hans E M Christensen3, Britt Hedman2, Keith O Hodgson1,2, Edward I Solomon4,2.   

Abstract

Determining the requirements for efficient oxygen (O2) activation is key to understanding how enzymes maintain efficacy and mitigate unproductive, often detrimental reactivity. For the α-ketoglutarate (αKG)-dependent nonheme iron enzymes, both a concerted mechanism (both cofactor and substrate binding prior to reaction with O2) and a sequential mechanism (cofactor binding and reaction with O2 precede substrate binding) have been proposed. Deacetoxycephalosporin C synthase (DAOCS) is an αKG-dependent nonheme iron enzyme for which both of these mechanisms have been invoked to generate an intermediate that catalyzes oxidative ring expansion of penicillin substrates in cephalosporin biosynthesis. Spectroscopy shows that, in contrast to other αKG-dependent enzymes (which are six coordinate when only αKG is bound to the FeII), αKG binding to FeII-DAOCS results in ∼45% five-coordinate sites that selectively react with O2 relative to the remaining six-coordinate sites. However, this reaction produces an FeIII species that does not catalyze productive ring expansion. Alternatively, simultaneous αKG and substrate binding to FeII-DAOCS produces five-coordinate sites that rapidly react with O2 to form an FeIV=O intermediate that then reacts with substrate to produce cephalosporin product. These results demonstrate that the concerted mechanism is operative in DAOCS and by extension, other nonheme iron enzymes.

Entities:  

Keywords:  concerted mechanism; metalloenzymes; oxygen activation; oxygenase chemistry

Year:  2020        PMID: 32094179      PMCID: PMC7071927          DOI: 10.1073/pnas.1922484117

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  45 in total

1.  Alternative reactivity of an alpha-ketoglutarate-dependent iron(II) oxygenase: enzyme self-hydroxylation.

Authors:  A Liu; R Y Ho; L Que; M J Ryle; B S Phinney; R P Hausinger
Journal:  J Am Chem Soc       Date:  2001-05-30       Impact factor: 15.419

2.  Kinetic dissection of the catalytic mechanism of taurine:alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli.

Authors:  John C Price; Eric W Barr; Lee M Hoffart; Carsten Krebs; J Martin Bollinger
Journal:  Biochemistry       Date:  2005-06-07       Impact factor: 3.162

3.  Probing the penicillin sidechain selectivity of recombinant deacetoxycephalosporin C synthase.

Authors:  A Dubus; M D Lloyd; H J Lee; C J Schofield; J E Baldwin; J M Frere
Journal:  Cell Mol Life Sci       Date:  2001-05       Impact factor: 9.261

4.  Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of α-Heteroatom Assistance.

Authors:  Noah P Dunham; Wei-Chen Chang; Andrew J Mitchell; Ryan J Martinie; Bo Zhang; Jonathan A Bergman; Lauren J Rajakovich; Bo Wang; Alexey Silakov; Carsten Krebs; Amie K Boal; J Martin Bollinger
Journal:  J Am Chem Soc       Date:  2018-06-04       Impact factor: 15.419

Review 5.  The biosynthesis of penicillins and cephalosporins.

Authors:  J E Baldwin; E Abraham
Journal:  Nat Prod Rep       Date:  1988-04       Impact factor: 13.423

6.  Evidence for Modulation of Oxygen Rebound Rate in Control of Outcome by Iron(II)- and 2-Oxoglutarate-Dependent Oxygenases.

Authors:  Juan Pan; Eliott S Wenger; Megan L Matthews; Christopher J Pollock; Minakshi Bhardwaj; Amelia J Kim; Benjamin D Allen; Robert B Grossman; Carsten Krebs; J Martin Bollinger
Journal:  J Am Chem Soc       Date:  2019-09-16       Impact factor: 15.419

7.  Structure of a cephalosporin synthase.

Authors:  K Valegård; A C van Scheltinga; M D Lloyd; T Hara; S Ramaswamy; A Perrakis; A Thompson; H J Lee; J E Baldwin; C J Schofield; J Hajdu; I Andersson
Journal:  Nature       Date:  1998-08-20       Impact factor: 49.962

8.  The structural basis of cephalosporin formation in a mononuclear ferrous enzyme.

Authors:  Karin Valegård; Anke C Terwisscha van Scheltinga; Alain Dubus; Graziella Ranghino; Linda M Oster; Janos Hajdu; Inger Andersson
Journal:  Nat Struct Mol Biol       Date:  2003-12-29       Impact factor: 15.369

9.  Characterization of extradiol dioxygenases from a polychlorinated biphenyl-degrading strain that possess higher specificities for chlorinated metabolites.

Authors:  Frédéric H Vaillancourt; María-Amparo Haro; Nathalie M Drouin; Zamil Karim; Halim Maaroufi; Lindsay D Eltis
Journal:  J Bacteriol       Date:  2003-02       Impact factor: 3.490

10.  Substrate-triggered formation and remarkable stability of the C-H bond-cleaving chloroferryl intermediate in the aliphatic halogenase, SyrB2.

Authors:  Megan L Matthews; Courtney M Krest; Eric W Barr; Frédéric H Vaillancourt; Christopher T Walsh; Michael T Green; Carsten Krebs; J Martin Bollinger
Journal:  Biochemistry       Date:  2009-05-26       Impact factor: 3.162

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  5 in total

Review 1.  Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families.

Authors:  Madison B Berger; Alice R Walker; Erik Antonio Vázquez-Montelongo; G Andrés Cisneros
Journal:  Phys Chem Chem Phys       Date:  2021-10-13       Impact factor: 3.945

2.  Substrate-Specific Coupling of O2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases.

Authors:  Sarah G Pati; Charlotte E Bopp; Hans-Peter E Kohler; Thomas B Hofstetter
Journal:  ACS Catal       Date:  2022-05-16       Impact factor: 13.700

3.  Anaerobic fixed-target serial crystallography.

Authors:  Patrick Rabe; John H Beale; Agata Butryn; Pierre Aller; Anna Dirr; Pauline A Lang; Danny N Axford; Stephen B Carr; Thomas M Leissing; Michael A McDonough; Bradley Davy; Ali Ebrahim; Julien Orlans; Selina L S Storm; Allen M Orville; Christopher J Schofield; Robin L Owen
Journal:  IUCrJ       Date:  2020-08-21       Impact factor: 4.769

4.  Mechanisms of O2 Activation by Mononuclear Non-Heme Iron Enzymes.

Authors:  Edward I Solomon; Dory E DeWeese; Jeffrey T Babicz
Journal:  Biochemistry       Date:  2021-07-15       Impact factor: 3.162

Review 5.  Spectroscopic and in vitro Investigations of Fe2+ /α-Ketoglutarate-Dependent Enzymes Involved in Nucleic Acid Repair and Modification.

Authors:  David Schmidl; Niko S W Lindlar Né Jonasson; Annika Menke; Sabine Schneider; Lena J Daumann
Journal:  Chembiochem       Date:  2022-02-15       Impact factor: 3.461

  5 in total

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