1
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Song DY, Stubbe J, Nocera DG. Protein engineering a PhotoRNR chimera based on a unifying evolutionary apparatus among the natural classes of ribonucleotide reductases. Proc Natl Acad Sci U S A 2024; 121:e2317291121. [PMID: 38648489 PMCID: PMC11067019 DOI: 10.1073/pnas.2317291121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/19/2024] [Indexed: 04/25/2024] Open
Abstract
Ribonucleotide reductases (RNRs) are essential enzymes that catalyze the de novo transformation of nucleoside 5'-di(tri)phosphates [ND(T)Ps, where N is A, U, C, or G] to their corresponding deoxynucleotides. Despite the diversity of factors required for function and the low sequence conservation across RNRs, a unifying apparatus consolidating RNR activity is explored. We combine aspects of the protein subunit simplicity of class II RNR with a modified version of Escherichia coli class la photoRNRs that initiate radical chemistry with light to engineer a mimic of a class II enzyme. The design of this RNR involves fusing a truncated form of the active site containing α subunit with the functionally important C-terminal tail of the radical-generating β subunit to render a chimeric RNR. Inspired by a recent cryo-EM structure, a [Re] photooxidant is located adjacent to Y356[β], which is an essential component of the radical transport pathway in class I RNRs. Combination of this RNR photochimera with cytidine diphosphate (CDP), adenosine triphosphate (ATP), and light resulted in the generation of Y356• along with production of deoxycytidine diphosphate (dCDP) and cytosine. The photoproducts reflect an active site chemistry consistent with both the consensus mechanism of RNR and chemistry observed when RNR is inactivated by mechanism-based inhibitors in the active site. The enzymatic activity of the RNR photochimera in the absence of any β metallocofactor highlights the adaptability of the 10-stranded αβ barrel finger loop to support deoxynucleotide formation and accommodate the design of engineered RNRs.
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Affiliation(s)
- David Y. Song
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - JoAnne Stubbe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
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2
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Greene BL, Kang G, Cui C, Bennati M, Nocera DG, Drennan CL, Stubbe J. Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets. Annu Rev Biochem 2020; 89:45-75. [PMID: 32569524 PMCID: PMC7316142 DOI: 10.1146/annurev-biochem-013118-111843] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the de novo conversion of nucleotides to deoxynucleotides in all organisms, controlling their relative ratios and abundance. In doing so, they play an important role in fidelity of DNA replication and repair. RNRs' central role in nucleic acid metabolism has resulted in five therapeutics that inhibit human RNRs. In this review, we discuss the structural, dynamic, and mechanistic aspects of RNR activity and regulation, primarily for the human and Escherichia coli class Ia enzymes. The unusual radical-based organic chemistry of nucleotide reduction, the inorganic chemistry of the essential metallo-cofactor biosynthesis/maintenance, the transport of a radical over a long distance, and the dynamics of subunit interactions all present distinct entry points toward RNR inhibition that are relevant for drug discovery. We describe the current mechanistic understanding of small molecules that target different elements of RNR function, including downstream pathways that lead to cell cytotoxicity. We conclude by summarizing novel and emergent RNR targeting motifs for cancer and antibiotic therapeutics.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Chang Cui
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Department of Chemistry, University of Göttingen, 37073 Göttingen, Germany
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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3
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Ryzhkova EP. Alternative enzymes as a special strategy for the adaptation of procaryotic organisms (Review). APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Nelissen FHT, Tessari M, Wijmenga SS, Heus HA. Stable isotope labeling methods for DNA. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 96:89-108. [PMID: 27573183 DOI: 10.1016/j.pnmrs.2016.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
NMR is a powerful method for studying proteins and nucleic acids in solution. The study of nucleic acids by NMR is far more challenging than for proteins, which is mainly due to the limited number of building blocks and unfavorable spectral properties. For NMR studies of DNA molecules, (site specific) isotope enrichment is required to facilitate specific NMR experiments and applications. Here, we provide a comprehensive review of isotope-labeling strategies for obtaining stable isotope labeled DNA as well as specifically stable isotope labeled building blocks required for enzymatic DNA synthesis.
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Affiliation(s)
- Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Marco Tessari
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Sybren S Wijmenga
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands.
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5
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Spataru T, Fernandez F. The Nature of the Co-C Bond Cleavage Processes in Methylcob(II)Alamin and Adenosylcob(III)Alamin. CHEMISTRY JOURNAL OF MOLDOVA 2016. [DOI: 10.19261/cjm.2016.11(1).01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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6
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Garabato BD, Kumar N, Lodowski P, Jaworska M, Kozlowski PM. Electronically excited states of cob(ii)alamin: insights from CASSCF/XMCQDPT2 and TD-DFT calculations. Phys Chem Chem Phys 2016; 18:4513-26. [DOI: 10.1039/c5cp06439b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The low-lying excited states of cob(ii)alamin were investigated using time-dependent density functional theory (TD-DFT), and multiconfigurational CASSCF/XMCQDPT2 methodology, to help understand their role in B12-mediated reactions.
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Affiliation(s)
| | - Neeraj Kumar
- Department of Chemistry
- University of Louisville
- Louisville
- USA
- Pacific Northwest National Laboratory
| | - Piotr Lodowski
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice
- Poland
| | - Maria Jaworska
- Department of Theoretical Chemistry
- Institute of Chemistry
- University of Silesia
- PL-40 006 Katowice
- Poland
| | - Pawel M. Kozlowski
- Department of Chemistry
- University of Louisville
- Louisville
- USA
- Visiting Professor at the Department of Food Sciences
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7
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Lundin D, Berggren G, Logan DT, Sjöberg BM. The origin and evolution of ribonucleotide reduction. Life (Basel) 2015; 5:604-36. [PMID: 25734234 PMCID: PMC4390871 DOI: 10.3390/life5010604] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 11/16/2022] Open
Abstract
Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs.
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Affiliation(s)
- Daniel Lundin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Gustav Berggren
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden.
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden.
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8
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Menon BRK, Menon N, Fisher K, Rigby SEJ, Leys D, Scrutton NS. Glutamate 338 is an electrostatic facilitator of C-Co bond breakage in a dynamic/electrostatic model of catalysis by ornithine aminomutase. FEBS J 2015; 282:1242-55. [PMID: 25627283 PMCID: PMC4413051 DOI: 10.1111/febs.13215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 01/04/2023]
Abstract
How cobalamin-dependent enzymes promote C–Co homolysis to initiate radical catalysis has been debated extensively. For the pyridoxal 5′-phosphate and cobalamin-dependent enzymes lysine 5,6-aminomutase and ornithine 4,5-aminomutase (OAM), large-scale re-orientation of the cobalamin-binding domain linked to C–Co bond breakage has been proposed. In these models, substrate binding triggers dynamic sampling of the B12-binding Rossmann domain to achieve a catalytically competent ‘closed’ conformational state. In ‘closed’ conformations of OAM, Glu338 is thought to facilitate C–Co bond breakage by close association with the cobalamin adenosyl group. We investigated this using stopped-flow continuous-wave photolysis, viscosity dependence kinetic measurements, and electron paramagnetic resonance spectroscopy of a series of Glu338 variants. We found that substrate-induced C–Co bond homolysis is compromised in Glu388 variant forms of OAM, although photolysis of the C–Co bond is not affected by the identity of residue 338. Electrostatic interactions of Glu338 with the 5′-deoxyadenosyl group of B12 potentiate C–Co bond homolysis in ‘closed’ conformations only; these conformations are unlocked by substrate binding. Our studies extend earlier models that identified a requirement for large-scale motion of the cobalamin domain. Our findings indicate that large-scale motion is required to pre-organize the active site by enabling transient formation of ‘closed’ conformations of OAM. In ‘closed’ conformations, Glu338 interacts with the 5′-deoxyadenosyl group of cobalamin. This interaction is required to potentiate C–Co homolysis, and is a crucial component of the approximately 1012 rate enhancement achieved by cobalamin-dependent enzymes for C–Co bond homolysis.
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Affiliation(s)
- Binuraj R K Menon
- Biotechnology and Biological Sciences Research Council/Engineering and Physical Sciences Research Council Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, UK
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9
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Photolytic cleavage of Co–C bond: A mechanistic study for the formation of solvent coordinated cobalt(II) complex. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2013.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Wang M, Warncke K. Entropic origin of cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase. J Am Chem Soc 2013; 135:15077-84. [PMID: 24028405 PMCID: PMC3839591 DOI: 10.1021/ja404467d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adenosylcobalamin-dependent enzymes accelerate the cleavage of the cobalt-carbon (Co-C) bond of the bound coenzyme by >10(10)-fold. The cleavage-generated 5'-deoxyadenosyl radical initiates the catalytic cycle by abstracting a hydrogen atom from substrate. Kinetic coupling of the Co-C bond cleavage and hydrogen-atom-transfer steps at ambient temperatures has interfered with past experimental attempts to directly address the factors that govern Co-C bond cleavage catalysis. Here, we use time-resolved, full-spectrum electron paramagnetic resonance spectroscopy, with temperature-step reaction initiation, starting from the enzyme-coenzyme-substrate ternary complex and (2)H-labeled substrate, to study radical pair generation in ethanolamine ammonia-lyase from Salmonella typhimurium at 234-248 K in a dimethylsulfoxide/water cryosolvent system. The monoexponential kinetics of formation of the (2)H- and (1)H-substituted substrate radicals are the same, indicating that Co-C bond cleavage rate-limits radical pair formation. Analysis of the kinetics by using a linear, three-state model allows extraction of the microscopic rate constant for Co-C bond cleavage. Eyring analysis reveals that the activation enthalpy for Co-C bond cleavage is 32 ± 1 kcal/mol, which is the same as for the cleavage reaction in solution. The origin of Co-C bond cleavage catalysis in the enzyme is, therefore, the large, favorable activation entropy of 61 ± 6 cal/(mol·K) (relative to 7 ± 1 cal/(mol·K) in solution). This represents a paradigm shift from traditional, enthalpy-based mechanisms that have been proposed for Co-C bond-breaking in B12 enzymes. The catalysis is proposed to arise from an increase in protein configurational entropy along the reaction coordinate.
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Affiliation(s)
- Miao Wang
- Department of Physics, Emory University, Atlanta, GA 30322, United States
- Current Address: Wilmad-LabGlass, 1172 NW Boulevard, Vineland, NJ 08360
| | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, GA 30322, United States
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11
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Kozlowski PM, Kumar M, Piecuch P, Li W, Bauman NP, Hansen JA, Lodowski P, Jaworska M. The Cobalt–Methyl Bond Dissociation in Methylcobalamin: New Benchmark Analysis Based on Density Functional Theory and Completely Renormalized Coupled-Cluster Calculations. J Chem Theory Comput 2012; 8:1870-94. [DOI: 10.1021/ct300170y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pawel M. Kozlowski
- Department of Chemistry, University
of Louisville,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Manoj Kumar
- Department of Chemistry, University
of Louisville,
2320 South Brook St., Louisville, Kentucky 40292, United States
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Wei Li
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Nicholas P. Bauman
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Jared A. Hansen
- Department of Chemistry, Michigan State University,
578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Piotr Lodowski
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
| | - Maria Jaworska
- Institute
of Chemistry, University of Silesia, Szkolna
9, PL-40 006 Katowice, Poland
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12
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Abstract
Vitamin B12, the "antipernicious anaemia factor", is a crystallisable cobalt-complex, which belongs to a group of unique "complete" corrinoids, named cobalamins (Cbl). In humans, instead of the "vitamin", two organometallic B12-forms are coenzymes in two metabolically important enzymes: Methyl-cobalamin, the cofactor of methionine synthase, and coenzyme B12 (adenosyl-cobalamin), the cofactor of methylmalonyl-CoA mutase. The cytoplasmatic methionine synthase catalyzes the transfer of a methyl group from N-methyl-tetrahydrofolate to homocysteine to yield methionine and to liberate tetrahydrofolate. In the mitochondrial methylmalonyl-CoA mutase a radical process transforms methylmalonyl-CoA (a remains e.g. from uneven numbered fatty acids) into succinyl-CoA, for further metabolic use. In addition, in the human mitochondria an adenosyl-transferase incorporates the organometallic group of coenzyme B12. In all these enzymes, the bound B12-derivatives engage (or are formed) in exceptional organometallic enzymatic reactions. This chapter recapitulates the physiological chemistry of vitamin B12, relevant in the context of the metabolic transformation of B12-derivatives into the relevant coenzyme forms and their use in B12-dependent enzymes.
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Affiliation(s)
- Bernhard Kräutler
- Institute of Organic Chemistry and Centre of Molecular Biosciences (CMBI), University of Innsbruck, Innsbruck, Austria,
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13
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Minnihan EC, Seyedsayamdost MR, Uhlin U, Stubbe J. Kinetics of radical intermediate formation and deoxynucleotide production in 3-aminotyrosine-substituted Escherichia coli ribonucleotide reductases. J Am Chem Soc 2011; 133:9430-40. [PMID: 21612216 PMCID: PMC3125130 DOI: 10.1021/ja201640n] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Escherichia coli ribonucleotide reductase is an α2β2 complex and catalyzes the conversion of nucleoside 5'-diphosphates (NDPs) to 2'-deoxynucleotides (dNDPs). The reaction is initiated by the transient oxidation of an active-site cysteine (C(439)) in α2 by a stable diferric tyrosyl radical (Y(122)•) cofactor in β2. This oxidation occurs by a mechanism of long-range proton-coupled electron transfer (PCET) over 35 Å through a specific pathway of residues: Y(122)•→ W(48)→ Y(356) in β2 to Y(731)→ Y(730)→ C(439) in α2. To study the details of this process, 3-aminotyrosine (NH(2)Y) has been site-specifically incorporated in place of Y(356) of β. The resulting protein, Y(356)NH(2)Y-β2, and the previously generated proteins Y(731)NH(2)Y-α2 and Y(730)NH(2)Y-α2 (NH(2)Y-RNRs) are shown to catalyze dNDP production in the presence of the second subunit, substrate (S), and allosteric effector (E) with turnover numbers of 0.2-0.7 s(-1). Evidence acquired by three different methods indicates that the catalytic activity is inherent to NH(2)Y-RNRs and not the result of copurifying wt enzyme. The kinetics of formation of 3-aminotyrosyl radical (NH(2)Y•) at position 356, 731, and 730 have been measured with all S/E pairs. In all cases, NH(2)Y• formation is biphasic (k(fast) of 9-46 s(-1) and k(slow) of 1.5-5.0 s(-1)) and kinetically competent to be an intermediate in nucleotide reduction. The slow phase is proposed to report on the conformational gating of NH(2)Y• formation, while the k(cat) of ~0.5 s(-1) is proposed to be associated with rate-limiting oxidation by NH(2)Y• of the subsequent amino acid on the pathway during forward PCET. The X-ray crystal structures of Y(730)NH(2)Y-α2 and Y(731)NH(2)Y-α2 have been solved and indicate minimal structural changes relative to wt-α2. From the data, a kinetic model for PCET along the radical propagation pathway is proposed.
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Affiliation(s)
- Ellen C. Minnihan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Ulla Uhlin
- Department of Molecular Biology, Swedish University of Agricultural Science, Uppsala Biomedical Center, Box 590, SE-75124 Uppsala, Sweden
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
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14
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Lockley WJS, Heys JR. Metal-catalysed hydrogen isotope exchange labelling: a brief overview. J Labelled Comp Radiopharm 2010. [DOI: 10.1002/jlcr.1851] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Larsson KM, Logan DT, Nordlund P. Structural basis for adenosylcobalamin activation in AdoCbl-dependent ribonucleotide reductases. ACS Chem Biol 2010; 5:933-42. [PMID: 20672854 DOI: 10.1021/cb1000845] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Class II ribonucleotide reductases (RNR) catalyze the formation of an essential thiyl radical by homolytic cleavage of the Co-C bond in their adenosylcobalamin (AdoCbl) cofactor. Several mechanisms for the dramatic acceleration of Co-C bond cleavage in AdoCbl-dependent enzymes have been advanced, but no consensus yet exists. We present the structure of the class II RNR from Thermotoga maritima in three complexes: (i) with allosteric effector dTTP, substrate GDP, and AdoCbl; (ii) with dTTP and AdoCbl; (iii) with dTTP, GDP, and adenosine. Comparison of these structures gives the deepest structural insights so far into the mechanism of radical generation and transfer for AdoCbl-dependent RNR. AdoCbl binds to the active site pocket, shielding the substrate, transient 5'-deoxyadenosyl radical and nascent thiyl radical from solution. The e-propionamide side chain of AdoCbl forms hydrogen bonds directly to the α-phosphate group of the substrate. This interaction appears to cause a "locking-in" of the cofactor, and it is the first observation of a direct cofactor-substrate interaction in an AdoCbl-dependent enzyme. The structures support an ordered sequential reaction mechanism with release or relaxation of AdoCbl on each catalytic cycle. A conformational change of the AdoCbl adenosyl ribose is required to allow hydrogen transfer to the catalytic thiol group. Previously proposed mechanisms for radical transfer in B12-dependent enzymes cannot fully explain the transfer in class II RNR, suggesting that it may form a separate class that differs from the well-characterized eliminases and mutases.
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Affiliation(s)
- Karl-Magnus Larsson
- Department of Biochemistry
and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Derek T. Logan
- Department of Biochemistry and Structural Biology, Lund University, Box 124, S-221 00 Lund, Sweden
| | - Pär Nordlund
- Department of Biochemistry
and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-171 77 Stockholm, Sweden
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16
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Kozlowski PM, Kamachi T, Kumar M, Nakayama T, Yoshizawa K. Theoretical Analysis of the Diradical Nature of Adenosylcobalamin Cofactor−Tyrosine Complex in B12-Dependent Mutases: Inspiring PCET-Driven Enzymatic Catalysis. J Phys Chem B 2010; 114:5928-39. [DOI: 10.1021/jp100573b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takashi Kamachi
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Manoj Kumar
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tomonori Nakayama
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, and Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
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17
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Lohman GJS, Stubbe J. Inactivation of Lactobacillus leichmannii ribonucleotide reductase by 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate: covalent modification. Biochemistry 2010; 49:1404-17. [PMID: 20088569 PMCID: PMC2855214 DOI: 10.1021/bi902132u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ribonucleotide reductase (RNR) from Lactobacillus leichmannii, a 76 kDa monomer using adenosylcobalamin (AdoCbl) as a cofactor, catalyzes the conversion of nucleoside triphosphates to deoxynucleotides and is rapidly (<30 s) inactivated by 1 equiv of 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate (F(2)CTP). [1'-(3)H]- and [5-(3)H]F(2)CTP were synthesized and used independently to inactivate RNR. Sephadex G-50 chromatography of the inactivation mixture revealed that 0.47 equiv of a sugar was covalently bound to RNR and that 0.71 equiv of cytosine was released. Alternatively, analysis of the inactivated RNR by SDS-PAGE without boiling resulted in 33% of RNR migrating as a 110 kDa protein. Inactivation of RNR with a mixture of [1'-(3)H]F(2)CTP and [1'-(2)H]F(2)CTP followed by reduction with NaBH(4), alkylation with iodoacetamide, trypsin digestion, and HPLC separation of the resulting peptides allowed isolation and identification by MALDI-TOF mass spectrometry (MS) of a (3)H/(2)H-labeled peptide containing C(731) and C(736) from the C-terminus of RNR accounting for 10% of the labeled protein. The MS analysis also revealed that the two cysteines were cross-linked to a furanone species derived from the sugar of F(2)CTP. Incubation of [1'-(3)H]F(2)CTP with C119S-RNR resulted in 0.3 equiv of sugar being covalently bound to the protein, and incubation with NaBH(4) subsequent to inactivation resulted in trapping of 2'-fluoro-2'-deoxycytidine. These studies and the ones in the preceding paper (DOI: 10.1021/bi9021318 ) allow proposal of a mechanism of inactivation of RNR by F(2)CTP involving multiple reaction pathways. The proposed mechanisms share many common features with F(2)CDP inactivation of the class I RNRs.
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Affiliation(s)
| | - JoAnne Stubbe
- To whom correspondence should be addressed. Tel: (617) 253-1814. Fax: (617) 258-7247.
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18
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Lohman GJS, Gerfen GJ, Stubbe J. Inactivation of Lactobacillus leichmannii ribonucleotide reductase by 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate: adenosylcobalamin destruction and formation of a nucleotide-based radical. Biochemistry 2010; 49:1396-403. [PMID: 20088568 PMCID: PMC2867335 DOI: 10.1021/bi9021318] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductase (RNR, 76 kDa) from Lactobacillus leichmannii is a class II RNR that requires adenosylcobalamin (AdoCbl) as a cofactor. It catalyzes the conversion of nucleoside triphosphates to deoxynucleotides and is 100% inactivated by 1 equiv of 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate (F(2)CTP) in <2 min. Sephadex G-50 chromatography of the inactivation reaction mixture for 2 min revealed that 0.47 equiv of a sugar moiety is covalently bound to RNR and 0.25 equiv of a cobalt(III) corrin is tightly associated, likely through a covalent interaction with C(419) (Co-S) in the active site of RNR [Lohman, G. J. S., and Stubbe, J. (2010) Biochemistry 49, DOI: 10.1021/bi902132u ]. After 1 h, a similar experiment revealed 0.45 equiv of the Co-S adduct associated with the protein. Thus, at least two pathways are associated with RNR inactivation: one associated with alkylation by the sugar of F(2)CTP and the second with AdoCbl destruction. To determine the fate of [1'-(3)H]F(2)CTP in the latter pathway, the reaction mixture at 2 min was reduced with NaBH(4) (NaB(2)H(4)) and the protein separated from the small molecules using a centrifugation device. The small molecules were dephosphorylated and analyzed by HPLC to reveal 0.25 equiv of a stereoisomer of cytidine, characterized by mass spectrometry and NMR spectroscopy, indicating the trapped nucleotide had lost both of its fluorides and gained an oxygen. High-field ENDOR studies with [1'-(2)H]F(2)CTP from the reaction quenched at 30 s revealed a radical that is nucleotide-based. The relationship between this radical and the trapped cytidine analogue provides insight into the nonalkylative pathway for RNR inactivation relative to the alkylative pathway.
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Affiliation(s)
- Gregory J. S. Lohman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Gary J. Gerfen
- Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Ullmann Building, Room 225, Bronx, NY 10461
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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19
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Li X, Chung LW, Paneth P, Morokuma K. DFT and ONIOM(DFT:MM) studies on Co-C bond cleavage and hydrogen transfer in B12-dependent methylmalonyl-CoA mutase. Stepwise or concerted mechanism? J Am Chem Soc 2009; 131:5115-25. [PMID: 19309090 DOI: 10.1021/ja807677z] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The considerable protein effect on the homolytic Co-C bond cleavage to form the 5'-deoxyadenosyl (Ado) radical and cob(II)alamin and the subsequent hydrogen transfer from the methylmalonyl-CoA substrate to the Ado radical in the methylmalonyl-CoA mutase (MMCM) have been extensively studied by DFT and ONIOM(DFT/MM) methods. Several quantum models have been used to systematically study the protein effect. The calculations have shown that the Co-C bond dissociation energy is very much reduced in the protein, compared to that in the gas phase. The large protein effect can be decomposed into the cage effect, the effect of coenzyme geometrical distortion, and the protein MM effect. The largest contributor is the MM effect, which mainly consists of the interaction of the QM part of the coenzyme with the MM part of the coenzyme and the surrounding residues. In particular, Glu370 plays an important role in the Co-C bond cleavage process. These effects tremendously enhance the stability of the Co-C bond cleavage state in the protein. The initial Co-C bond cleavage and the subsequent hydrogen transfer were found to occur in a stepwise manner in the protein, although the concerted pathway for the Co-C bond cleavage coupled with the hydrogen transfer is more favored in the gas phase. The assumed concerted transition state in the protein has more deformation of the coenzyme and the substrate and has less interaction with the protein than the stepwise route. Key factors and residues in promoting the enzymatic reaction rate have been discussed in detail.
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Affiliation(s)
- Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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20
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Robertson WD, Warncke K. Photolysis of adenosylcobalamin and radical pair recombination in ethanolamine ammonia-lyase probed on the micro- to millisecond time scale by using time-resolved optical absorption spectroscopy. Biochemistry 2009; 48:140-7. [PMID: 19072291 DOI: 10.1021/bi801659e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The quantum yield and kinetics of decay of cob(II)alamin formed by pulsed-laser photolysis of adenosylcobalamin (AdoCbl; coenzyme B(12)) in AdoCbl-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium have been studied on the 10(-7)-10(-1) s time scale at 295 K by using transient ultraviolet-visible absorption spectroscopy. The aim is to probe the mechanism of formation and stabilization of the cob(II)alamin-5'-deoxyadenosyl radical pair, which is a key intermediate in EAL catalysis, and the influence of substrate binding on this process. Substrate binding is required for cobalt-carbon bond cleavage in the native system. Photolysis of AdoCbl in EAL leads to a quantum yield at 10(-7) s for cob(II)alamin of 0.08 +/- 0.01, which is 3-fold smaller than for AdoCbl in aqueous solution (0.23 +/- 0.01). The protein binding site therefore suppresses photoproduct radical pair formation. Three photoproduct states, P(f), P(s), and P(c), are identified in holo-EAL by the different cob(II)alamin decay kinetics (subscripts denote fast, slow, and constant, respectively). These states have the following first-order decay rate constants and quantum yields: 2.2 x 10(3) s(-1) and 0.02 for P(f), 4.2 x 10(2) s(-1) and 0.01 for P(s), and constant amplitude, with no recombination, and 0.05 for P(c), respectively. Binding of the substrate analogue (S)-1-amino-2-propanol to EAL eliminates the P(f) state and lowers the quantum yield of P(c) (0.03) relative to that of P(s) (0.01) but does not significantly change the quantum yield or decay rate constant of P(s), relative to those of holo-EAL. The substrate analogue thus influences the quantum yield at 10(-7) s by changing the cage escape rate from the geminate cob(II)alamin-5'-deoxyadenosyl radical pair state. However, the predicted substrate analogue binding-induced increase in the quantum yield is not observed. It is proposed that the substrate analogue does not induce the radical pair stabilizing changes in the protein that are characteristic of true substrates.
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21
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Jones AR, Hay S, Woodward JR, Scrutton NS. Magnetic field effect studies indicate reduced geminate recombination of the radical pair in substrate-bound adenosylcobalamin-dependent ethanolamine ammonia lyase. J Am Chem Soc 2007; 129:15718-27. [PMID: 18041840 DOI: 10.1021/ja077124x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The apparent conflict between literature evidence for (i) radical pair (RP) stabilization in adenosylcobalamin (AdoCbl)-dependent enzymes and (ii) the manifestation of magnetic field sensitivity due to appreciable geminate recombination of the RP has been reconciled by pre-steady-state magnetic field effect (MFE) investigations with ethanolamine ammonia lyase (EAL). We have shown previous stopped-flow MFE studies to be insensitive to magnetically induced changes in the net forward rate of C-Co homolytic bond cleavage. Subsequently, we observed a magnetic-dependence in the continuous-wave C-Co photolysis of free AdoCbl in 75% glycerol but have not done so in the thermal homolysis of this bond in the enzyme-bound cofactor in the presence of substrate. Consequently, in the enzyme-bound state, the RP generated upon homolysis appears to be stabilized against the extent of geminate recombination required to observe an MFE. These findings have strong implications for the mechanism of RP stabilization and the unprecedented catalytic power of this important class of cobalamin-dependent enzymes.
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Affiliation(s)
- Alex R Jones
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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22
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Affiliation(s)
- Stephen W Ragsdale
- Department of Biochemistry, Beadle Center, University of Nebraska, Lincoln, Nebraska 68588-0664, USA.
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23
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McDonough JE, Weir JJ, Sukcharoenphon K, Hoff CD, Kryatova OP, Rybak-Akimova EV, Scott BL, Kubas GJ, Mendiratta A, Cummins CC. Comparison of thermodynamic and kinetic aspects of oxidative addition of PhE-EPh (E = S, Se, Te) to Mo(CO)3(PR3)2, W(CO)3(PR3)2, and Mo(N[tBu]Ar)3 complexes. The role of oxidation state and ancillary ligands in metal complex induced chalcogenyl radical generation. J Am Chem Soc 2007; 128:10295-303. [PMID: 16881661 DOI: 10.1021/ja063250+] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enthalpies of oxidative addition of PhE-EPh (E = S, Se, Te) to the M(0) complexes M(PiPr3)2(CO)3 (M = Mo, W) to form stable complexes M(*EPh)(PiPr3)2(CO)3 are reported and compared to analogous data for addition to the Mo(III) complexes Mo(N[tBu]Ar)3 (Ar = 3,5-C6H3Me2) to form diamagnetic Mo(IV) phenyl chalcogenide complexes Mo(N[tBu]Ar)3(EPh). Reactions are increasingly exothermic based on metal complex, Mo(PiPr3)2(CO)3 < W(PiPr3)2(CO)3 < Mo(N[tBu]Ar)3, and in terms of chalcogenide, PhTe-TePh < PhSe-SePh < PhS-SPh. These data are used to calculate LnM-EPh bond strengths, which are used to estimate the energetics of production of a free *EPh radical when a dichalcogenide interacts with a specific metal complex. To test these data, reactions of Mo(N[tBu]Ar)3 and Mo(PiPr3)2(CO)3 with PhSe-SePh were studied by stopped-flow kinetics. First- and second-order dependence on metal ion concentration was determined for these two complexes, respectively, in keeping with predictions based on thermochemical data. ESR data are reported for the full set of bound chalcogenyl radical complexes (PhE*)M(PiPr3)2(CO)3; g values increase on going from S to Se, to Te, and from Mo to W. Calculations of electron densities of the SOMO show increasing electron density on the chalcogen atom on going from S to Se to Te. The crystal structure of W(*TePh)(PiPr3)2(CO)3 is reported.
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24
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Study of the spectroscopic characteristics of methyl (ligand) cobaloximes and their antibacterial activity. J CHEM SCI 2007. [DOI: 10.1007/s12039-007-0005-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Cheng MC, Marsh ENG. Evidence for coupled motion and hydrogen tunneling of the reaction catalyzed by glutamate mutase. Biochemistry 2007; 46:883-9. [PMID: 17223710 PMCID: PMC2518312 DOI: 10.1021/bi0616908] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that catalyze unusual isomerizations that proceed through organic radical intermediates generated by homolytic fission of the coenzyme's unique cobalt-carbon bond. These enzymes are part of a larger family of enzymes that catalyze radical chemistry in which a key step is the abstraction of a hydrogen atom from an otherwise inert substrate. To gain insight into the mechanism of hydrogen transfer, we previously used pre-steady-state, rapid-quench techniques to measure the alpha-secondary tritium kinetic and equilibrium isotope effects associated with the formation of 5'-deoxyadenosine when glutamate mutase was reacted with [5'-(3)H]adenosylcobalamin and L-glutamate. We showed that both the kinetic and equilibrium isotope effects are large and inverse, 0.76 and 0.72, respectively. We have now repeated these measurements using glutamate deuterated in the position of hydrogen abstraction. The effect of introducing a primary deuterium kinetic isotope effect on the hydrogen transfer step is to reduce the magnitude of the secondary kinetic isotope effect to a value close to unity, 1.05 +/- 0.08, whereas the equilibrium isotope effect is unchanged. The significant reduction in the secondary kinetic isotope effect is consistent with motions of the 5'-hydrogen atoms being coupled in the transition state to the motion of the hydrogen undergoing transfer, in a reaction that involves a large degree of quantum tunneling.
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Affiliation(s)
| | - E. Neil G. Marsh
- Correspondence should be addressed to this author at: Department of Chemistry, University of Michigan, Ann Arbor, MI 48109−1055, USA Tel (734) 763 6096 FAX (734) 764 8815 e-mail
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26
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Yoon M, Patwardhan A, Qiao C, Mansoorabadi SO, Menefee AL, Reed GH, Marsh ENG. Reaction of adenosylcobalamin-dependent glutamate mutase with 2-thiolglutarate. Biochemistry 2006; 45:11650-7. [PMID: 16981724 PMCID: PMC2517135 DOI: 10.1021/bi061067n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have investigated the reaction of glutamate mutase with the glutamate analogue, 2-thiolglutarate. In the standard assay, 2-thiolglutarate behaves as a competitive inhibitor with a Ki of 0.05 mM. However, rather than simply binding inertly at the active site, 2-thiolglutarate elicits cobalt-carbon bond homolysis and the formation of 5'-deoxyadenosine. The enzyme exhibits a complicated EPR spectrum in the presence of 2-thiolglutarate that is markedly different from any previously observed with the enzyme. The spectrum was simulated well by assuming that it arises from electron-electron spin coupling between a thioglycolyl radical and low-spin Co2+ in cob(II)alamin. Analysis of the zero-field splitting parameters obtained from the simulations places the organic radical approximately 10 A from the cobalt and at a tilt angle of approximately 70 degrees to the normal of the corrin ring. This orientation is in good agreement with that expected from the crystal structure of glutamate mutase complexed with the substrate. 2-Thiolglutarate appears to react in a manner analogous to that of glutamate by first forming a thiolglutaryl radical at C-4 that then undergoes fragmentation to produce acrylate and the sulfur-stabilized thioglycolyl radical. The thioglycolyl radical accumulates on the enzyme, suggesting it is too stable to undergo further steps in the mechanism at a detectable rate.
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Affiliation(s)
- Miri Yoon
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, WI 48109−1055, USA
| | - Anjali Patwardhan
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, WI 48109−1055, USA
| | - Chunhua Qiao
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, WI 48109−1055, USA
| | | | - Ann L. Menefee
- Department of Biochemistry, University of Wisconsin, Madison, MI 53726−4087, USA
| | - George H. Reed
- Department of Biochemistry, University of Wisconsin, Madison, MI 53726−4087, USA
| | - E. Neil G. Marsh
- Departments of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, WI 48109−1055, USA
- Correspondence should be addressed to this author at: Department of Chemistry, University of Michigan, Ann Arbor, MI 48109−1055, USA Tel (734) 763 6096 FAX (734) 764 8815 e-mail
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27
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Affiliation(s)
- Kenneth L Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens, 45701, USA.
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28
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Ren X, Alleyne BD, Djurovich PI, Adachi C, Tsyba I, Bau R, Thompson ME. Organometallic Complexes as Hole-Transporting Materials in Organic Light-Emitting Diodes. Inorg Chem 2004; 43:1697-707. [PMID: 14989662 DOI: 10.1021/ic035183f] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of metal complexes fac-tris(1-phenylpyrazolato-N,C(2)('))cobalt(III) [fac-Co(ppz)(3)], fac-tris(2-phenylpyridinato-N,C(2)(') cobalt(III) [fac-Co(ppy)(3)], and [tris[2-((pyrrole-2-ylmethylidene)amino)ethyl]amine]gallium(III) [Ga(pma)] as materials for hole-transporting layers (HTL) in organic light-emitting diodes (OLEDs) is reported. Co(ppz)(3) and Co(ppy)(3) were prepared by following literature procedures and isolated as mixtures of facial (fac) and meridional (mer) isomers. The more stable fac isomers were separated from the unstable mer forms via column chromatography and thermal gradient sublimation. Crystals of fac-Co(ppz)(3) are monoclinic, space group P2(1)/c, with a = 13.6121(12) A, b = 15.5600(12) A, c = 22.9603(17) A, beta = 100.5 degrees, V = 4781.3(7) A(3), and Z = 8. [Tris[2-((pyrrol-2-ylmethylidene)amino)ethyl]amine]gallium [Ga(pma)] was prepared by the reaction of gallium(III) nitrate with the pmaH(3) ligand precursor in methanol. Ga(pma) crystallizes in the cubic space group I3d with cell parameters a = 20.2377(4) A, b = 20.2377(4) A, c = 20.2377(4) A, beta = 90.0 degrees, V = 8288.6(3) A(3), and Z = 16. These cobalt and gallium complexes are pale colored to colorless solids, with optical energy gaps ranging 2.6-3.36 eV. A two-layer HTL/ETL (ETL = electron-transporting layer) device structure using fac-Co(ppz)(3) and fac-Co(ppy)(3) as the HTL does not give efficient electroluminescence. However, the introduction of a thin layer of a hole-transporting material (N,N'-bis(1-naphthyl)-N,N'-diphenylbenzidine, NPD) as an energy "stair-step" and electron/exciton-blocker dramatically improves the device performance. Both fac-Co(ppz)(3) and fac-Co(ppy)(3) devices give external quantum efficiencies higher than 1.0%, with brightness 5000 and 7000 Cd/m(2) at 10 V, respectively. Ga(pma) also functions as an efficient interface layer, giving device performances very similar to those of analogous devices using NPD as the interface layer. Stability tests have been carried out for Co(ppz)(3)/NPD/Alq(3) and Co(ppy)(3)/NPD/Alq(3) devices. While fac-Co(ppy)(3) gave stable OLEDs, the fac-Co(ppz)(3)-based devices had very short lifetimes. On the basis of the experimental results of chemical oxidation of fac-Co(ppz)(3), the major cause for the fast decay of the fac-Co(ppz)(3) device is proposed to be the decomposition of fac-Co(ppz)(3)(+) in the HTL layer during the device operation.
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Affiliation(s)
- Xiaofan Ren
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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29
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Ge J, Yu G, Ator MA, Stubbe J. Pre-steady-state and steady-state kinetic analysis of E. coli class I ribonucleotide reductase. Biochemistry 2003; 42:10071-83. [PMID: 12939135 DOI: 10.1021/bi034374r] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
E. coli ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates (NDPs) to dNDPs and is composed of two homodimeric subunits: R1 and R2. R1 binds NDPs and contains binding sites for allosteric effectors that control substrate specificity and turnover rate. R2 contains a diiron-tyrosyl radical (Y(*)) cofactor that initiates nucleotide reduction. Pre-steady-state experiments with wild type R1 or C754S/C759S-R1 and R2 were carried out to determine which step(s) are rate-limiting and whether both active sites of R1 can catalyze nucleotide reduction. Rapid chemical quench experiments monitoring dCDP formation gave k(obs) of 9 +/- 4 s(-1) with an amplitude of 1.7 +/- 0.4 equiv. This amplitude, generated in experiments with pre-reduced R1 (3 or 15 microM) in the absence of reductant, indicates that both monomers of R1 are active. Stopped-flow UV-vis spectroscopy monitoring the concentration of the Y(*) failed to reveal any changes from 2 ms to seconds under similar conditions. These pre-steady-state experiments, in conjunction with the steady-state turnover numbers for dCDP formation of 2-14 s(-1) at RNR concentrations of 0.05-0.4 microM (typical assay conditions), reveal that the rate-determining step is a physical step prior to rapid nucleotide reduction and rapid tyrosine reoxidation to Y(*). Steady-state experiments conducted at RNR concentrations of 3 and 15 microM, typical of pre-steady-state conditions, suggest that, in addition to the slow conformational change(s) prior to chemistry, re-reduction of the active site disulfide to dithiol or a conformational change accompanying this process can also be rate-limiting.
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Affiliation(s)
- Jie Ge
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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30
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Stubbe J, Nocera DG, Yee CS, Chang MCY. Radical initiation in the class I ribonucleotide reductase: long-range proton-coupled electron transfer? Chem Rev 2003; 103:2167-201. [PMID: 12797828 DOI: 10.1021/cr020421u] [Citation(s) in RCA: 667] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- JoAnne Stubbe
- Department of Chemistry, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA.
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31
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Doll KM, Fleming PE, Finke RG. The synthesis and characterization of 8-methoxy-5'-deoxyadenosylcobalamin: a coenzyme B(12) analog which, following Co-C bond homolysis, avoids cyclization of the 8-methoxy-5'-deoxyadenosyl radical. J Inorg Biochem 2002; 91:388-97. [PMID: 12161308 DOI: 10.1016/s0162-0134(02)00401-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The compound 8-methoxy-5'-deoxyadenosylcobalamin (8-MeOAdoCbl), has been synthesized in 37% yield and > or = 95% purity by HPLC, monitored at both 254 and 525 nm, or 90+/-2% purity as judged by the (1)H NMR spectrum of the aromatic cobalamin region. This is the first synthesis of this complex in which sufficient details are reported, where a yield and purity are reported, and where key problems in the synthesis and purification are overcome, so that 8-MeOAdoCbl can actually be obtained for use in other studies. Also demonstrated is the clean Co-C bond homolysis of 8-MeOAdoCbl to give initially 8-MeOAdoCbl and Co(II)Cbl in a UV-visible thermolysis experiment at 110 degrees C, results which show that the 8-MeO moiety suppresses the cyclization to the 8,5'-anhydro-adenosine otherwise seen for the adenosyl radical (Ado)*. Suppression of this cyclization pathway makes 8-MeOAdoCbl invaluable for studying the kinetic isotope effect (KIE) of the Ado* plus substrate H* abstraction reaction, a component of the first definitive test of Klinman's hypothesis that the optimization of enzyme catalysis may entail strategies that increase the probability of tunneling and thereby accelerate H* atom abstraction reaction rates.
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Affiliation(s)
- Kenneth M Doll
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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32
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White WT, Finke RG. Synthesis of adenosylcobinamide 2-chlorophenyl phosphate, a zwitterionic cobinamide phosphate analog of adenosylcobalamin en route to crystallizable cobinamides. J Inorg Biochem 2002; 91:371-87. [PMID: 12161307 DOI: 10.1016/s0162-0134(02)00402-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The design and implementation of a new, higher yield synthetic method for synthesizing zwitterionic cobinamide phosphates is described. Adenosylcobinamide 2-chlorophenyl phosphate, beta-AdoCbi-PAr -- a 5,6-dimethylbenzimidazole-free adenosylcobalamin analog, where a 2-chlorophenyl group replaces the ribofuranose and 5,6-dimethylbenzimidazole moieties -- is prepared in tens of milligram quantities, quantities sufficient for crystallization and enzyme trials, amounts 100-fold greater than previously available. The use of (31)P NMR spectroscopy to follow reactions directly, the use of control reactions to learn how to reduce reactant water content, and the use of reaction solvents that completely dissolved the corrinoid reactants were crucial for developing this new synthetic route. beta-AdoCbi-PAr was synthesized in 10% overall isolated yield from cyanocobinamide. Cyanocobinamide was converted to cyanocobinamide 2-chlorophenyl phosphate by direct phosphorylation with 2-chlorophenyl phosphodi-(1,2,4-triazolide) in 25% isolated yield and > or = 98% purity. Sodium borohydride reduction of cyanocobinamide 2-chlorophenyl phosphate and reaction with 5'-chloro-5'-deoxy-adenosine produced beta-AdoCbi-PAr in 42% yield and > or = 98% purity. These compounds were characterized by HPLC, (1)H and (31)P NMR, UV-visible spectroscopy, and liquid secondary ionization mass spectroscopy.
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Affiliation(s)
- Wesley T White
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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33
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Randaccio L, Geremia S, Stener M, Toffoli D, Zangrando E. Electronic Properties of the Axial Co−C and Co−S Bonds in B12 Systems − A Density Functional Study. Eur J Inorg Chem 2002. [DOI: 10.1002/1099-0682(20021)2002:1<93::aid-ejic93>3.0.co;2-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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34
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Fontecave M, Mulliez E, Ollagnier-de-Choudens S. Adenosylmethionine as a source of 5'-deoxyadenosyl radicals. Curr Opin Chem Biol 2001; 5:506-11. [PMID: 11578923 DOI: 10.1016/s1367-5931(00)00237-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The combination of an iron-sulfur cluster and S-adenosylmethionine provides a novel mechanism for the initiation of radical catalysis in an unanticipated variety of metabolic processes. Molecular details of the cluster-mediated reductive cleavage of S-adenosylmethionine to methionine and, presumably, a 5'-deoxyadenosyl radical are the targets of recent studies.
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Affiliation(s)
- M Fontecave
- Laboratoire de Chimie et Biochimie des Centres Rédox Biologiques, DBMS-CB, CEA/CNRS/Université Joseph Fourier, UMR 5047, 17 Avenue des Martyrs, 38054 Grenoble, Cedex 09, France.
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35
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Marsh EN, Drennan CL. Adenosylcobalamin-dependent isomerases: new insights into structure and mechanism. Curr Opin Chem Biol 2001; 5:499-505. [PMID: 11578922 DOI: 10.1016/s1367-5931(00)00238-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Adenosylcobalamin-dependent isomerases catalyze a variety of chemically difficult 1,2-rearrangements that proceed through a mechanism involving free radical intermediates. These radicals are initially generated by homolysis of the cobalt-carbon bond of the coenzyme. Recently, the crystal structures of several of these enzymes have been solved, revealing two modes of coenzyme binding and highlighting the role of the protein in controlling the rearrangement of reactive substrate radical intermediates. Complementary data from kinetic, spectroscopic and theoretical studies have produced insights into the mechanism by which substrate radicals are generated at the active site, and the pathways by which they rearrange.
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Affiliation(s)
- E N Marsh
- Department of Chemistry and Division of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
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36
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Affiliation(s)
- M Fontecave
- Laboratoire de Chimie et Biochimie des Centres Rédox Biologiques, DBMS-CEA, CNRS, Université Joseph Fourier, Grenoble, 38054, France
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37
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Huhta MS, Chen HP, Hemann C, Hille CR, Marsh EN. Protein-coenzyme interactions in adenosylcobalamin-dependent glutamate mutase. Biochem J 2001; 355:131-7. [PMID: 11256957 PMCID: PMC1221720 DOI: 10.1042/0264-6021:3550131] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glutamate mutase catalyses an unusual isomerization involving free-radical intermediates that are generated by homolysis of the cobalt-carbon bond of the coenzyme adenosylcobalamin (coenzyme B(12)). A variety of techniques have been used to examine the interaction between the protein and adenosylcobalamin, and between the protein and the products of coenzyme homolysis, cob(II)alamin and 5'-deoxyadenosine. These include equilibrium gel filtration, isothermal titration calorimetry, and resonance Raman, UV-visible and EPR spectroscopies. The thermodynamics of adenosylcobalamin binding to the protein have been examined and appear to be entirely entropy-driven, with DeltaS=109 J.mol(-1).K(-1). The cobalt-carbon bond stretching frequency is unchanged upon coenzyme binding to the protein, arguing against a ground-state destabilization of the cobalt-carbon bond of adenosylcobalamin by the protein. However, reconstitution of the enzyme with cob(II)alamin and 5'-deoxyadenosine, the two stable intermediates formed subsequent to homolysis, results in the blue-shifting of two of the bands comprising the UV-visible spectrum of the corrin ring. The most plausible interpretation of this result is that an interaction between the protein, 5'-deoxyadenosine and cob(II)alamin introduces a distortion into the ring corrin that perturbs its electronic properties.
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Affiliation(s)
- M S Huhta
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, U.S.A
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38
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Affiliation(s)
- E N Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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39
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Abstract
Adenosylcobalamin (coenzyme B12)-dependent glutamate mutase catalyzes a most unusual carbon skeleton rearrangement involving the isomerization of l-glutamate to L-threo-methylaspartate, a reaction that is without precedent in organic chemistry. This reaction proceeds through a mechanism involving free radical intermediates that are initiated by homolysis of the cobalt-carbon bond of the coenzyme. The enzyme serves as a paradigm for adenosylcobalamin-dependent catalysis and, more generally, provides insights into how enzymes generate and control reactive free radical species. This review describes how recent studies on the mechanism and structure of glutamate mutase have contributed to our understanding of adenosylcobalamin-mediated catalysis. Copyright 2000 Academic Press.
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Affiliation(s)
- EN Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109-1055
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40
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Sirovatka JM, Rappé AK, Finke RG. Molecular mechanics studies of coenzyme B12 complexes with constrained CoN(axial-base) bond lengths: introduction of the universal force field (UFF) to coenzyme B12 chemistry and its use to probe the plausibility of an axial-base-induced, ground-state corrin butterfly conformational steric effect. Inorganica Chim Acta 2000. [DOI: 10.1016/s0020-1693(00)00025-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Sirovatka JM, Finke RG. Hydrogen abstraction from thiols by adenosyl radicals: chemical precedent for thiyl radical formation, the first catalytic step in ribonucleoside triphosphate reductase from Lactobacillus leichmannii. J Inorg Biochem 2000; 78:149-60. [PMID: 10766338 DOI: 10.1016/s0162-0134(99)00224-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Aqueous solutions of adenosylcobalamin (AdoCbl) were thermolyzed with excess beta-mercaptoethanol under anaerobic conditions. The product studies reveal that approximately 90% Co-C bond homolysis occurs, to yield Co(II)cobalamin, 5'-deoxyadenosine, and the disulfide product from the combination of two HOCH2CH2S* radicals, 2,2'-dithiodiethanol; there is also approximately 10% Co-C bond heterolysis, yielding Co(III)cobalamin, adenine, and 2,3-dihydroxy-4-pentenal. The kinetic studies show there is a first-order dependence on AdoCbl and zero-order dependence on thiol under the higher [RSH] experimental conditions used, consistent with the rate-determining step at high [RSH] being the generation of Ado*. The kinetic results require that, in enzyme-free AdoCbl solution, adenosyl radical (Ado*) is formed as a discrete intermediate which then abstracts H* from the added thiol. The activation parameters for Co-C bond homolysis in the presence of thiol trap are the same within experimental error as the activation parameters for Co-C bond homolysis without trap, standard delta H(obs) = 29(2) kcal mol(-1) and standard delta S(obs) = -1(5) e.u. The results, in comparison to the rate of Co-C bond homolysis in ribonucleoside triphosphate reductase (RTPR), reveal that RTPR accelerates Co-C bond cleavage in AdoCbl by approximately 10(10+/-1). The recent literature evidence bearing on the exact mechanism of RTPR enzymic cleavage of the Co-C bond of AdoCbl is briefly discussed, notably the fact that this mechanism is presently controversial, but does involve at least coupled (and possibly concerted) Co-C cleavage, -S-H cleavage, and C-H (Ado-H) formation steps.
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Affiliation(s)
- J M Sirovatka
- Chemistry Department, Colorado State University, Ft. Collins 80523, USA
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42
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Maiti N, Widjaja L, Banerjee R. Proton transfer from histidine 244 may facilitate the 1,2 rearrangement reaction in coenzyme B(12)-dependent methylmalonyl-CoA mutase. J Biol Chem 1999; 274:32733-7. [PMID: 10551831 DOI: 10.1074/jbc.274.46.32733] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methylmalonyl-CoA mutase is an adenosylcobalamin-dependent enzyme that catalyzes the 1,2 rearrangement of methylmalonyl-CoA to succinyl-CoA. This reaction results in the interchange of a carbonyl-CoA group and a hydrogen atom on vicinal carbons. The crystal structure of the enzyme reveals the presence of an aromatic cluster of residues in the active site that includes His-244, Tyr-243, and Tyr-89 in the large subunit. Of these, His-244 is within hydrogen bonding distance to the carbonyl oxygen of the carbonyl-CoA moiety of the substrate. The location of these aromatic residues suggests a possible role for them in catalysis either in radical stabilization and/or by direct participation in one or more steps in the reaction. The mechanism by which the initially formed substrate radical isomerizes to the product radical during the rearrangement of methylmalonyl-CoA to succinyl-CoA is unknown. Ab initio molecular orbital theory calculations predict that partial proton transfer can contribute significantly to the lowering of the barrier for the rearrangement reaction. In this study, we report the kinetic characterization of the H244G mutant, which results in an acute sensitivity of the enzyme to oxygen, indicating the important role of this residue in radical stabilization. Mutation of His-244 leads to an approximately 300-fold lowering in the catalytic efficiency of the enzyme and loss of one of the two titratable pK(a) values that govern the activity of the wild type enzyme. These data suggest that protonation of His-244 increases the reaction rate in wild type enzyme and provides experimental support for ab initio molecular orbital theory calculations that predict rate enhancement of the rearrangement reaction by the interaction of the migrating group with a general acid. However, the magnitude of the rate enhancement is significantly lower than that predicted by the theoretical studies.
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Affiliation(s)
- N Maiti
- Biochemistry Department, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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43
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Brown KL, Zou X. Thermolysis of coenzymes B12 at physiological temperatures: activation parameters for cobalt-carbon bond homolysis and a quantitative analysis of the perturbation of the homolysis equilibrium by the ribonucleoside triphosphate reductase from Lactobacillus leichmannii. J Inorg Biochem 1999; 77:185-95. [PMID: 10643658 DOI: 10.1016/s0162-0134(99)00190-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The kinetics of the thermolysis of 5'-deoxyadenosylcobalamin (AdoCbl, coenzyme B12) in aqueous solution, pH 7.5, have been studied in the temperature range 30-85 degrees C using AdoCbl tritiated at the adenine C2 position and the method of initial rates. Combined with a careful analysis of the distribution of adenine-containing products, the results permit the dissection of the competing rate constants for carbon-cobalt bond homolysis and heterolysis. After correction for the temperature-dependent occurrence of the much less reactive base-off species of AdoCbl, the activation parameters for homolysis of the base-on species were found to be delta H++homo,on = 33.8 +/- 0.2 kcal mol-1 and delta S++homo,on = 13.5 +/- 0.7 cal mol-1 K-1, values not significantly different from those determined by Hay and Finke (J. Am. Chem. Soc. 108 (1986) 4820), in the temperature range 85-115 degrees C. In contrast, the heterolysis of base-on AdoCbl was characterized by a much smaller enthalpy of activation (delta H++het,on = 18.5 +/- 0.2 kcal mol-1) and a negative entropy of activation (delta S++het,on = -34.0 +/- 0.7 cal mol-1 K-1) so that heterolysis, which is minor pathway at elevated temperatures, is the dominant pathway for AdoCbl decomposition at physiological temperatures. Using literature values for the rate constant for the reverse reaction, the equilibrium constant for AdoCbl homolysis at 37 degrees C was calculated to be 7.9 x 10(-18). Comparison with the equilibrium constant for this homolysis at the active site of the ribonucleoside triphosphate reductase from Lactobacillus leichmannii shows that the enzymes shifts the equilibrium constant towards homolysis products by a factor of 2.9 x 10(12) (17.7 kcal mol-1) by binding the thermolysis products with an equilibrium constant of 7.1 x 10(16) M-2, compared to the bonding constant for AdoCbl of 2.4 x 10(4) M-1.
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Affiliation(s)
- K L Brown
- Department of Chemistry and Biochemistry, Ohio University, Athens 45701, USA.
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44
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Brasch NE, Hsu TL, Doll KM, Finke RG. Synthesis and characterization of isolable thiolatocobalamin complexes relevant to coenzyme B12-dependent ribonucleoside triphosphate reductase. J Inorg Biochem 1999; 76:197-209. [PMID: 10605837 DOI: 10.1016/s0162-0134(99)00128-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The syntheses, isolation and characterization of cyclohexylthiolatocobalamin (C6H11SCbl), glutathionylcobalamin (GluSCbl), and cysteinylcobalamin (CysSCbl) are reported in 75, 55, and 65% yield, respectively. Characterization was achieved using elemental analyses, L-SIMS (liquid secondary ion mass spectrometry), UV-visible spectroscopy and, for the more stable C6H11SCbl and GluSCbl, our recently established 1H NMR method (which emphasizes the readily interpreted aromatic region of the cobalamin's 1H NMR spectrum). Preliminary evidence is presented for clean homolysis of the RS-Co bond in C6H11SCbl, GluSCbl, and CysSCbl to give RS. and .Co(II)Cbl radical pairs analogous to those that are intermediates in ribonucleoside triphosphate reductase (RTPR). A summary is provided which emphasizes the seven variables identified to date, underlying the successful syntheses and isolation of thiolatocobalamins, variables which make the one-step syntheses of RSCbls considerably more complex than they initially appear. Also briefly discussed are the analogous protein-S-Cbl complexes that are seen as side-products in RTPR, and the probability that such side-products are formed when HOCbl.HX is used as a possible 'active-site inhibitor' complex with B12-dependent enzymes.
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Affiliation(s)
- N E Brasch
- Department of Chemistry, Colorado State University, Fort Collins 80523, USA
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45
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Rangel M, Arcos T, de Castro B. Photolysis Primary Products of Alkylcobaloximes Controlled by the Cobalt−Carbon Bond Strength. Organometallics 1999. [DOI: 10.1021/om990078s] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Rangel
- Instituto de Ciências Biomédicas de Abel Salazar, CEQUP, 4050 Porto, Portugal, and Departamento de Química, Faculdade de Ciências, CEQUP, 4150 Porto, Portugal
| | - Teresa Arcos
- Instituto de Ciências Biomédicas de Abel Salazar, CEQUP, 4050 Porto, Portugal, and Departamento de Química, Faculdade de Ciências, CEQUP, 4150 Porto, Portugal
| | - Baltazar de Castro
- Instituto de Ciências Biomédicas de Abel Salazar, CEQUP, 4050 Porto, Portugal, and Departamento de Química, Faculdade de Ciências, CEQUP, 4150 Porto, Portugal
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46
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Lawrence CC, Gerfen GJ, Samano V, Nitsche R, Robins MJ, Rétey J, Stubbe J. Binding of Cob(II)alamin to the adenosylcobalamin-dependent ribonucleotide reductase from Lactobacillus leichmannii. Identification of dimethylbenzimidazole as the axial ligand. J Biol Chem 1999; 274:7039-42. [PMID: 10066759 DOI: 10.1074/jbc.274.11.7039] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribonucleoside triphosphate reductase (RTPR) from Lactobacillus leichmannii catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates and uses coenzyme B12, adenosylcobalamin (AdoCbl), as a cofactor. Use of a mechanism-based inhibitor, 2'-deoxy-2'-methylenecytidine 5'-triphosphate, and isotopically labeled RTPR and AdoCbl in conjunction with EPR spectroscopy has allowed identification of the lower axial ligand of cob(II)alamin when bound to RTPR. In common with the AdoCbl-dependent enzymes catalyzing irreversible heteroatom migrations and in contrast to the enzymes catalyzing reversible carbon skeleton rearrangements, the dimethylbenzimidazole moiety of the cofactor is not displaced by a protein histidine upon binding to RTPR.
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Affiliation(s)
- C C Lawrence
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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