Research Topics
Genomes and Genes | J StubbeSummaryAffiliation: Massachusetts Institute of Technology Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case studyJoseph A Cotruvo
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
Metallomics 4:1020-36. 2012..We propose that, in many of the systems discussed, "discrimination" between metals is not performed by the protein itself, but it is instead determined by the environment in which the protein is expressed...- Growth and localization of polyhydroxybutyrate granules in Ralstonia eutrophaMorgan Beeby
California Institute of Technology, Pasadena, California, USA
J Bacteriol 194:1092-9. 2012..Previous thin-section electron microscopy (EM), fluorescence microscopy, and atomic force microscopy (AFM) results to the contrary may reflect both differences in nucleoid condensation and specimen preparation-induced artifacts... 
Harnessing free radicals: formation and function of the tyrosyl radical in ribonucleotide reductaseJ Stubbe
Dept of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
Trends Biochem Sci 23:438-43. 1998..The Escherichia coli RNR cofactor provides a paradigm for cofactors in other di-iron requiring or tyrosyl-radical-requiring proteins...- Polyhydroxyalkanoate (PHA) hemeostasis: the role of PHA synthaseJoAnne Stubbe
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Nat Prod Rep 20:445-57. 2003.... - Nontemplate-dependent polymerization processes: polyhydroxyalkanoate synthases as a paradigmJoAnne Stubbe
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Annu Rev Biochem 74:433-80. 2005..These enzymes are of interest as they generate biodegradable polymers. Our current knowledge of PHA production and utilization in vitro and in vivo as well as the contribution of many proteins to these processes will be reviewed... - The evolution of ribonucleotide reduction revisitedJ Stubbe
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambrige, MA 02139, USA
Trends Biochem Sci 26:93-9. 2001.... - Ribonucleotide reductases: the link between an RNA and a DNA world?J Stubbe
Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Curr Opin Struct Biol 10:731-6. 2000..The common structures and the common complex-radical-based chemistry of these systems, as well as of the class II RNRs, suggest that RNRs evolved by divergent evolution and provide an essential link between the RNA and DNA world... - Radical initiation in the class I ribonucleotide reductase: long-range proton-coupled electron transfer?JoAnne Stubbe
Department of Chemistry, 77 Massachusetts Avenue, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 4307, USA
Chem Rev 103:2167-201. 2003 - Control of metallation and active cofactor assembly in the class Ia and Ib ribonucleotide reductases: diiron or dimanganese?JoAnne Stubbe
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
Curr Opin Chem Biol 15:284-90. 2011..The presence of the class Ib RNR in numerous pathogenic bacteria also highlights the importance of manganese for these organisms' growth and virulence... - High-field EPR detection of a disulfide radical anion in the reduction of cytidine 5'-diphosphate by the E441Q R1 mutant of Escherichia coli ribonucleotide reductaseC C Lawrence
Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 96:8979-84. 1999..These experiments demonstrate that high-field time-domain EPR spectroscopy is a powerful new tool for deconvolution of a mixture of radical species... - N5-carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coliE J Mueller
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 33:2269-78. 1994..N5-CAIR has a half-life of 0.9 min at pH 7.8 and 30 degrees C. Thus, two new enzymatic activities and a new intermediate have been discovered in the de novo purine biosynthetic pathway of E. coli... - Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutaseE Meyer
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
Biochemistry 38:3012-8. 1999..The mechanistic implications of these results relative to the PurE-only (CO2- and AIR-requiring) AIR carboxylases are discussed... - Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase by time-resolved physical biochemical methods and X-ray crystallographyW Tong
Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
Biochemistry 37:5840-8. 1998..Studies with two mutants, Y356F and double mutant Y356F and Y122F R2, are interpreted in terms of the possible role of Y356 in the putative electron transfer reaction between the R1 and R2 subunits of this RNR... - PHA synthase from chromatium vinosum: cysteine 149 is involved in covalent catalysisU Müh
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
Biochemistry 38:826-37. 1999..004 wt % activity and was capable of making polymer. A mechanism is proposed in which PhaC contains all the elements essential for catalysis and the polymerization proceeds by covalent catalysis using C149 and potentially C130... - Solution structure of Co(III)-bleomycin-OOH bound to a phosphoglycolate lesion containing oligonucleotide: implications for bleomycin-induced double-strand DNA cleavageS T Hoehn
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Biochemistry 40:5894-905. 2001..Two cis conformations of these protons are also observed, and ROESY experiments provide evidence for interconversion of all of these forms. The relationship of these observations to the model for ds cleavage is presented... - Why multiple small subunits (Y2 and Y4) for yeast ribonucleotide reductase? Toward understanding the role of Y4J Ge
Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 98:10067-72. 2001..8-1.3 micromol.min.mg. Titration of Y2 with Y4 in the presence of Fe(2+) and O(2) gives maximal activity with one equivalent of Y4 per Y2. Models for the function of Y4 based on these data and the accompanying structure will be discussed... - Mechanistic studies on class I polyhydroxybutyrate (PHB) synthase from Ralstonia eutropha: class I and III synthases share a similar catalytic mechanismY Jia
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Biochemistry 40:1011-9. 2001..These studies, in conjunction with search algorithms for secondary structure, suggest that the Class I and III synthases are mechanistically similar and structurally homologous, despite their physical and kinetic differences... - Mechanism-based inhibition of a mutant Escherichia coli ribonucleotide reductase (cysteine-225----serine) by its substrate CDPS S Mao
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
Proc Natl Acad Sci U S A 86:1485-9. 1989..7% the rate of wild-type B1. When dithiothreitol is utilized as reductant, however, the rate of CDP reduction with [Ser759]B1 is identical to that observed with wild type... - Formylglycinamide ribonucleotide synthetase from Escherichia coli: cloning, sequencing, overproduction, isolation, and characterizationF J Schendel
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 28:2459-71. 1989..Incubation of [18O]FGAR with enzyme, ATP, and glutamine results in quantitative transfer of the 18O to Pi... - The function of adenosylcobalamin in the mechanism of ribonucleoside triphosphate reductase from Lactobacillus leichmanniiC C Lawrence
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
Curr Opin Chem Biol 2:650-5. 1998.... - Mechanism of assembly of the tyrosyl radical-dinuclear iron cluster cofactor of ribonucleotide reductaseJ M Bollinger
Department of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge 02139
Science 253:292-8. 1991..Unlike reactions catalyzed by heme-iron peroxidases, oxygenases, and model complexes, the reconstitution reaction appears not to involve high-valent iron intermediates... - Class I and III polyhydroxyalkanoate synthases from Ralstonia eutropha and Allochromatium vinosum: characterization and substrate specificity studiesW Yuan
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Arch Biochem Biophys 394:87-98. 2001..The results suggest that in vitro, both PHA synthases are very specific and provide further support for their active site structural similarities. In vitro results differ from studies in vivo... - Identification of an active site residue of the R1 subunit of ribonucleotide reductase from Escherichia coli: characterization of substrate-induced polypeptide cleavage by C225SR1W A van der Donk
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
Biochemistry 35:10058-67. 1996..The localization of the residues at the cleavage site of C225SR1 provides a biochemical identification of the active site region of the R1 subunit of RDPR from E.coli. The details of the mechanism of cleavage remain to be elucidated... - Investigation of the mechanism of phosphoribosylamine transfer from glutamine phosphoribosylpyrophosphate amidotransferase to glycinamide ribonucleotide synthetaseJ Rudolph
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 34:2241-50. 1995..These results suggest that the requisite channeling interaction between PRPP-AT and GAR-syn, which is indicated by the kinetic results, must be a transient one... - Characterization of C439SR1, a mutant of Escherichia coli ribonucleotide diphosphate reductase: evidence that C439 is a residue essential for nucleotide reduction and C439SR1 is a protein possessing novel thioredoxin-like activityS S Mao
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 31:9752-9. 1992..Its additional cysteines, presumably C754 and C759, appear to function as a thioredoxin with the wt-R1, even though it is incapacitated with respect to nucleotide reduction... - Purification of ribonucleotide reductase subunits Y1, Y2, Y3, and Y4 from yeast: Y4 plays a key role in diiron cluster assemblyH H Nguyen
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 96:12339-44. 1999..30 micromol.min(-1).mg(-1). Studies with antibodies to Y4 and Y2 reveal that they can form a complex in vivo. Y4 appears to play an important role in diiron-Y. assembly of Y2... - Lipases provide a new mechanistic model for polyhydroxybutyrate (PHB) synthases: characterization of the functional residues in Chromatium vinosum PHB synthaseY Jia
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Biochemistry 39:3927-36. 2000..The relationship of the lipase model to previous models based on fatty acid synthases is discussed... - Cloning, sequencing, and expression of the adenosylcobalamin-dependent ribonucleotide reductase from Lactobacillus leichmanniiS Booker
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
Proc Natl Acad Sci U S A 90:8352-6. 1993..5 g of bacteria. Initial characterization of the recombinant RTPR indicates that its properties are identical to those of the RTPR isolated from L. leichmannii... - Direct observation of a transient tyrosine radical competent for initiating turnover in a photochemical ribonucleotide reductaseSteven Y Reece
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
J Am Chem Soc 129:13828-30. 2007 - Site-specific insertion of 3-aminotyrosine into subunit alpha2 of E. coli ribonucleotide reductase: direct evidence for involvement of Y730 and Y731 in radical propagationMohammad R Seyedsayamdost
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
J Am Chem Soc 129:15060-71. 2007..The observed NH2Y. may constitute the first detection of an amino acid radical intermediate in the proposed radical propagation pathway during turnover... - Modular evolution of the purine biosynthetic pathwayT J Kappock
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue 18 409, Cambridge, MA 02139, USA
Curr Opin Chem Biol 4:567-72. 2000.... - Proton-coupled electron transfer: the mechanistic underpinning for radical transport and catalysis in biologySteven Y Reece
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 6-335 Cambridge, MA 02139-4307, USA
Philos Trans R Soc Lond B Biol Sci 361:1351-64. 2006.... - Site-specific replacement of Y356 with 3,4-dihydroxyphenylalanine in the beta2 subunit of E. coli ribonucleotide reductaseMohammad R Seyedsayamdost
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, 02139 4307, USA
J Am Chem Soc 128:2522-3. 2006..They further show that substrate binding brings about rapid conformational changes which place the complex into its active form(s) and suggest that the RNR complex is asymmetric... - Use of 3-aminotyrosine to examine the pathway dependence of radical propagation in Escherichia coli ribonucleotide reductaseEllen C Minnihan
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
Biochemistry 48:12125-32. 2009..2-0.3% of that observed at 731 and 730, and with (c), no NH(2)Y(*) was observed. These studies suggest the evolution of an optimized pathway of conserved Ys in the oxidation of C(439)... - Forward and reverse electron transfer with the Y356DOPA-beta2 heterodimer of E. coli ribonucleotide reductaseMohammad R Seyedsayamdost
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
J Am Chem Soc 129:2226-7. 2007 - Generation of the R2 subunit of ribonucleotide reductase by intein chemistry: insertion of 3-nitrotyrosine at residue 356 as a probe of the radical initiation processCyril S Yee
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 42:14541-52. 2003..Under all conditions, the pK(a) was minimally perturbed. This has important mechanistic implications for the radical initiation process... - Site-specific incorporation of fluorotyrosines into the R2 subunit of E. coli ribonucleotide reductase by expressed protein ligationMohammad R Seyedsayamdost
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
Nat Protoc 2:1225-35. 2007..Ligation of the 22-mer peptide to the thioester-activated R2 and subsequent purification yield full-length R2 with the F(n)Y at residue 356. The procedure to generate 100 mg quantities of Y356F(n)Y-R2 takes 3-4 months... - Pre-steady-state and steady-state kinetic analysis of E. coli class I ribonucleotide reductaseJie Ge
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 42:10071-83. 2003.... - Glycinamide ribonucleotide synthetase from Escherichia coli: cloning, overproduction, sequencing, isolation, and characterizationY S Cheng
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 29:218-27. 1990..Incubation of [18O]glycine, ATP, and PRA results in quantitative transfer of the 18O to Pi. GAR synthetase is very specific for its substrate glycine... - Mono-, di-, tri-, and tetra-substituted fluorotyrosines: new probes for enzymes that use tyrosyl radicals in catalysisMohammad R Seyedsayamdost
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
J Am Chem Soc 128:1569-79. 2006.... - pH Rate profiles of FnY356-R2s (n = 2, 3, 4) in Escherichia coli ribonucleotide reductase: evidence that Y356 is a redox-active amino acid along the radical propagation pathwayMohammad R Seyedsayamdost
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
J Am Chem Soc 128:1562-8. 2006.... - Photoactive peptides for light-initiated tyrosyl radical generation and transport into ribonucleotide reductaseSteven Y Reece
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
J Am Chem Soc 129:8500-9. 2007.... 
Structural examination of the transient 3-aminotyrosyl radical on the PCET pathway of E. coli ribonucleotide reductase by multifrequency EPR spectroscopyMohammad R Seyedsayamdost
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
J Am Chem Soc 131:15729-38. 2009..This analysis is an essential first step in using the detailed structure of NH(2)Y(730)* to formulate a model for a PCET mechanism within alpha2 and for use of NH(2)Y in other systems where transient Y*s participate in catalysis...- Nanosecond generation of tyrosyl radicals via laser-initiated decaging of oxalate-modified amino acidsMichelle C Y Chang
Department of Chemistry, 6-335, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA
J Org Chem 67:6820-2. 2002..This approach provides unnatural caged amino acids that may be incorporated into model and biological systems for the study of proton-coupled electron transfer in enzymatic catalysis... - Identification of protonated oxygenic ligands of ribonucleotide reductase intermediate XMuralidharan Shanmugam
Department of Chemistry, Northwestern University, Evanston, Illinois 60208 3113, USA
J Am Chem Soc 131:3370-6. 2009.... - Methodology to probe subunit interactions in ribonucleotide reductasesA Quamrul Hassan
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 47:13046-55. 2008..4 microM for subunit interaction. Disruption of the interaction of the alpha2-DAN-beta2 complex is accompanied by a decrease in fluorescence intensity and can serve as a high-throughput screen for inhibitors of subunit interactions... - PELDOR spectroscopy with DOPA-beta2 and NH2Y-alpha2s: distance measurements between residues involved in the radical propagation pathway of E. coli ribonucleotide reductaseMohammad R Seyedsayamdost
Department of Chemistry and Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
J Am Chem Soc 129:15748-9. 2007..Further, they support a long-range radical initiation process for C439* generation and provide a structural constraint for residue Y356, which is thermally labile in all beta2 structures solved to date... - Importance of the maintenance pathway in the regulation of the activity of Escherichia coli ribonucleotide reductaseDaniela Hristova
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 47:3989-99. 2008..Whole cell Mössbauer analysis on cells induced with 0.5 mM arabinose supports high iron loading in beta. These results suggest that modulation of the level of Y (*) in vivo in E. coli is a mechanism of regulating RNR activity... - Electron transfer reactions of fluorotyrosyl radicalsSteven Y Reece
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
J Am Chem Soc 128:13654-5. 2006..These data demonstrate that fluorotyrosines will be powerful probes for unraveling charge transport mechanisms in enzymes that utilize tyrosyl radicals... - New insight into the role of the PhaP phasin of Ralstonia eutropha in promoting synthesis of polyhydroxybutyrateG M York
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
J Bacteriol 183:2394-7. 2001.... - Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformationS T Hoehn
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
Nucleic Acids Res 29:3413-23. 2001..The coupling constants further allowed assignment of an unusual sugar pucker for each anomer. The unique position of the abasic site in our structural model for each anomer is discussed in terms of repair of such lesions in vivo... - NrdI, a flavodoxin involved in maintenance of the diferric-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductaseJoseph A Cotruvo
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 105:14383-8. 2008..Data presented support the presence of a distinct maintenance pathway for NrdEF, orthogonal to that for NrdAB involving YfaE... - Mapping the subunit interface of ribonucleotide reductase (RNR) using photo cross-linkingA Quamrul Hassan
Department of Chemistry, Massachusetts Institute of Technology, 77 Mass Avenue, Cambridge, MA 02139, USA
Bioorg Med Chem Lett 18:5923-5. 2008..The third contained the same beta peptide and a peptide in alpha found in its alphaD helix. These results provide direct support for the proposed docking model of alpha2beta2... - Re(bpy)(CO)3CN as a probe of conformational flexibility in a photochemical ribonucleotide reductaseSteven Y Reece
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
Biochemistry 48:5832-8. 2009.... - Enhanced subunit interactions with gemcitabine-5'-diphosphate inhibit ribonucleotide reductasesJun Wang
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 104:14324-9. 2007..This information and the proposed asymmetry between the interactions of alphanbetan provide an explanation for complete inactivation of RNR with substoichiometric amounts of F2CDP... - Mechanism of inactivation of human ribonucleotide reductase with p53R2 by gemcitabine 5'-diphosphateJun Wang
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 48:11612-21. 2009..Analysis of the inactivated wt-alpha/beta' RNR by size exclusion chromatography indicates a quaternary structure of alpha6beta'6. A mechanism of inactivation common with halpha/beta is presented... - Bleomycins: towards better therapeuticsJingyang Chen
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Nat Rev Cancer 5:102-12. 2005.... - Turning on ribonucleotide reductase by light-initiated amino acid radical generationMichelle C Y Chang
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 4307, USA
Proc Natl Acad Sci U S A 101:6882-7. 2004..These results provide direct evidence for the chemical competence of aromatic amino acid radicals and the importance of Y356 in R2 in the radical initiation process of the class I RNRs... - Inactivation of Lactobacillus leichmannii ribonucleotide reductase by 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate: adenosylcobalamin destruction and formation of a nucleotide-based radicalGregory J S Lohman
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 49:1396-403. 2010..The relationship between this radical and the trapped cytidine analogue provides insight into the nonalkylative pathway for RNR inactivation relative to the alkylative pathway... - Detection of intermediates from the polymerization reaction catalyzed by a D302A mutant of class III polyhydroxyalkanoate (PHA) synthaseJiamin Tian
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Biochemistry 44:1495-503. 2005..05 microm) were observed in contrast to the 0.2-0.5 microm granules observed with the wt strain. Use of the D302A synthase has allowed successful interrogation of the initiation and elongation steps catalyzed by the class III synthase... - Insight into the mechanism of inactivation of ribonucleotide reductase by gemcitabine 5'-diphosphate in the presence or absence of reductantErin Artin
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 48:11622-9. 2009..The EPR features are very similar to those we recently reported for the nucleotide radical generated with CDP and E441Q-RNR... - Di-iron-tyrosyl radical ribonucleotide reductasesJoAnne Stubbe
Chemistry and Department, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
Curr Opin Chem Biol 7:183-8. 2003..Recent advances include Insight into the function of the tyrosyl radical in initiation of nucleotide reduction... - In vitro analysis of the chain termination reaction in the synthesis of poly-(R)-beta-hydroxybutyrate by the class III synthase from Allochromatium vinosumAdam G Lawrence
Department of Biology, Biomaterials Science and Engineering Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biomacromolecules 6:2113-9. 2005..In the first, NAC liberated at the active site during polymerization acts as a chain transfer agent. In the second, there is a noncovalent polymer intermediate covalently linked to NAC, which can dissociate from the active site... - Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathwayE Meyer
Department of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 31:5022-32. 1992..No dependence on the concentration of HCO3- could be demonstrated. A new energy requirement in the purine biosynthetic pathway has been established... - The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimerMichael D Sintchak
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Nat Struct Biol 9:293-300. 2002..Thus, L. leichmannii RNR is a paradigm for the simplest structural entity capable of ribonucleotide reduction, a reaction linking the RNA and DNA worlds... - Replacement of Y730 and Y731 in the alpha2 subunit of Escherichia coli ribonucleotide reductase with 3-aminotyrosine using an evolved suppressor tRNA/tRNA-synthetase pairMohammad R Seyedsayamdost
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Methods Enzymol 462:45-76. 2009.... - Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox-active tyrosines in ribonucleotide reductaseKenichi Yokoyama
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 4307, USA
J Am Chem Soc 132:8385-97. 2010.... - The Ralstonia eutropha PhaR protein couples synthesis of the PhaP phasin to the presence of polyhydroxybutyrate in cells and promotes polyhydroxybutyrate productionGregory M York
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
J Bacteriol 184:59-66. 2002..Models for regulatory roles of PhaR in regulating PhaP and promoting PHA production are presented... - Class III polyhydroxybutyrate synthase: involvement in chain termination and reinitiationJiamin Tian
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Biochemistry 44:8369-77. 2005..The results from studies under both sets of conditions suggest that an inherent property of the synthase is chain termination and reinitiation... - YfaE, a ferredoxin involved in diferric-tyrosyl radical maintenance in Escherichia coli ribonucleotide reductaseChia Hung Wu
Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 46:11577-88. 2007..The titrations and kinetic studies provide the first evidence for a protein involved in the maintenance pathway and likely the biosynthetic pathway... - Site-specific replacement of a conserved tyrosine in ribonucleotide reductase with an aniline amino acid: a mechanistic probe for a redox-active tyrosineMichelle C Y Chang
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
J Am Chem Soc 126:16702-3. 2004.... - An active dimanganese(III)-tyrosyl radical cofactor in Escherichia coli class Ib ribonucleotide reductaseJoseph A Cotruvo
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 49:1297-309. 2010..We propose that NrdI is an essential player in E. coli class Ib RNR cluster assembly and that the Mn(III)(2)-Y* cofactor, not the diferric-Y* one, is the active metallocofactor in vivo... - Kinetic studies of polyhydroxybutyrate granule formation in Wautersia eutropha H16 by transmission electron microscopyJiamin Tian
Department of Chemistry, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
J Bacteriol 187:3814-24. 2005..The extent of protein coverage of the granule surface area is presented in the accompanying paper... - Analysis of transient polyhydroxybutyrate production in Wautersia eutropha H16 by quantitative Western analysis and transmission electron microscopyJiamin Tian
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts 02139, USA
J Bacteriol 187:3825-32. 2005..The TEM studies of wild-type and deltaphaR strains in TSB provided further support for an alternative mechanism of granule formation... - Detection of covalent and noncovalent intermediates in the polymerization reaction catalyzed by a C149S class III polyhydroxybutyrate synthasePing Li
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Biochemistry 48:9202-11. 2009..Thus, the (HB)(n)CoA analogues function as kinetically and chemically competent intermediates. These results support the mechanism involving covalently and noncovalently bound intermediates... - 2,3-difluorotyrosine at position 356 of ribonucleotide reductase R2: a probe of long-range proton-coupled electron transferCyril S Yee
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
J Am Chem Soc 125:10506-7. 2003..8). pH rate profiles (pH 6.5-9.0) of wild-type and F2Y-R2 were very similar. Thus, a proton can be lost from the putative PCET pathway without affecting nucleotide reduction. The current model involving H* transfer is thus unlikely... - Determination of the in vivo stoichiometry of tyrosyl radical per betabeta' in Saccharomyces cerevisiae ribonucleotide reductaseAllison D Ortigosa
Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 45:12282-94. 2006..Thus, under normal growth conditions, the cell assembles stoichiometric amounts of Y(*) and modulation of Y(*) concentration is not involved in the regulation of RNR activity... - Synthesis, characterization and solution structure of tethered oligonucleotides containing an internal 3'-phosphoglycolate, 5'-phosphate gapped lesionHans-Dieter Junker
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
Nucleic Acids Res 30:5497-508. 2002..Titrations of the lesioned GGCC oligomer with HOO-CoBLM leads to a mixture of complexes, in contrast to results of a similar titration with the lesioned GTAC oligomer... - Inactivation of Lactobacillus leichmannii ribonucleotide reductase by 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate: covalent modificationGregory J S Lohman
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 49:1404-17. 2010..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... - Transcriptional analysis of Ralstonia eutropha genes related to poly-(R)-3-hydroxybutyrate homeostasis during batch fermentationAdam G Lawrence
Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA
Appl Microbiol Biotechnol 68:663-72. 2005..No evidence of phaZ1c expression was found under the experimental conditions used in this study... - Bleomycins: new methods will allow reinvestigation of old issuesJingyang Chen
Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
Curr Opin Chem Biol 8:175-81. 2004..New methods offer new opportunities to revisit and solve old problems, which could ultimately lead to development of a more effective therapeutic... - Ralstonia eutropha H16 encodes two and possibly three intracellular Poly[D-(-)-3-hydroxybutyrate] depolymerase genesGregory M York
Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
J Bacteriol 185:3788-94. 2003..PhaZ2 is thus suggested to be an intracellular depolymerase. The role of PhaZ3 remains to be established... - The active form of the Saccharomyces cerevisiae ribonucleotide reductase small subunit is a heterodimer in vitro and in vivoDeborah L Perlstein
Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 44:15366-77. 2005..These studies together demonstrate that beta' plays a crucial role in cluster assembly in vitro and in vivo and that the active form of the yeast R2 is betabeta'... - N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysisAaron A Hoskins
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 46:2842-55. 2007..Subsequent movement of the aminoimidazole moiety of AIR reorients it for addition of CO2 at C4 to generate isoCAIR. His45 is now in a position to remove a C4 proton to produce CAIR... - Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sitesJingyang Chen
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Biochemistry 46:3096-107. 2007..The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed... - GC/MS methods to quantify the 2-deoxypentos-4-ulose and 3'-phosphoglycolate pathways of 4' oxidation of 2-deoxyribose in DNA: application to DNA damage produced by gamma radiation and bleomycinBingzi Chen
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Chem Res Toxicol 20:1701-8. 2007..For gamma radiation, on the other hand, 4' oxidation was found to comprise only 13% of 2-deoxyribose oxidation chemistry, with 3% oxAB (4 per 10(6) nt per Gy) and 10% 3PG (13 per 10(6) nt per Gy)... - DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamicsJingyang Chen
Department of Chemistry Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
Nucleic Acids Res 36:253-62. 2008..These results provide structural insight into the dynamics of abasic sites that are intrinsically modulated by the bases opposite the abasic site... - Mechanistic studies on bleomycin-mediated DNA damage: multiple binding modes can result in double-stranded DNA cleavageJingyang Chen
Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
Nucleic Acids Res 36:3781-90. 2008..The significance of the current study to understanding BLM's action in vivo is discussed... - Synthesis and characterization of oligonucleotides containing a 4'-keto abasic siteJingyang Chen
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Biochemistry 43:5278-86. 2004..The stability of duplex DNA containing a 4'-keto abasic site relative to an abasic site in the same sequence context is reported under physiological conditions... - EPR distance measurements support a model for long-range radical initiation in E. coli ribonucleotide reductaseMarina Bennati
Institute of Physical and Theoretical Chemistry and BMRZ, University of Frankfurt, D 60439 Frankfurt, Germany
J Am Chem Soc 127:15014-5. 2005..PELDOR and DQC paramagnetic resonance methods give rise to a distance of 48 A, similar to that calculated from a docking model of the R1 and R2 structures... - Pulsed ELDOR spectroscopy measures the distance between the two tyrosyl dadicals in the R2 subunit of the E. coli ribonucleotide reductaseMarina Bennati
Institute of Physical and Theoretical Chemistry, J. Goethe University of Frankfurt, D-60439 Frankfurt, Germany
J Am Chem Soc 125:14988-9. 2003..4 A) between the center of mass of the spin density distribution of each Y* on each R2 monomer from the structure. The experiments provide the first direct experimental evidence for two Y*'s in a single R2 in solution... - Subcellular localization of yeast ribonucleotide reductase regulated by the DNA replication and damage checkpoint pathwaysRuojin Yao
Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver 80262, USA
Proc Natl Acad Sci U S A 100:6628-33. 2003..These results suggest a mechanism by which DNA damage checkpoint modulates RNR activity through the temporal and spatial regulation of its subunits... - Structures of the yeast ribonucleotide reductase Rnr2 and Rnr4 homodimersMonika Sommerhalter
Department of Biochemistry, Northwestern University, Evanston, Illinois 60208, USA
Biochemistry 43:7736-42. 2004..When taken together, these results support a model in which Rnr4 stabilizes Rnr2 for cofactor assembly and activity... - Structure of the nitrogen-centered radical formed during inactivation of E. coli ribonucleotide reductase by 2'-azido-2'-deoxyuridine-5'-diphosphate: trapping of the 3'-ketonucleotideJörg Fritscher
Institute of Physical and Theoretical Chemistry, J W Goethe University of Frankfurt, and Center for Biological Magnetic Resonance, 60439 Frankfurt, Germany
J Am Chem Soc 127:7729-38. 2005..The results are most consistent with the R-S-N*-C-OH structure and provide evidence for the trapping of a 3'-ketonucleotide in the reduction process... - Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formationMariya Morar
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
Biochemistry 47:7816-30. 2008..The flexibility of the PurS dimer is proposed to play a role in the activation of the complex and the formation of the ammonia channel. A potential path for the ammonia channel is identified... - Nuclear localization of the Saccharomyces cerevisiae ribonucleotide reductase small subunit requires a karyopherin and a WD40 repeat proteinZhen Zhang
Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO 80045, USA
Proc Natl Acad Sci U S A 103:1422-7. 2006..Our results suggest that Wtm1 acts either as an adaptor to facilitate nuclear import of betabeta' by Kap122 or as an anchor to retain betabeta' in the nucleus... - Dif1 is a DNA-damage-regulated facilitator of nuclear import for ribonucleotide reductaseYang David Lee
Harvard Medical School, Department of Genetics, Brigham and Women s Hospital, Center for Genetics and Genomics, Howard Hughes Medical Institute, Boston, MA 02115, USA
Mol Cell 32:70-80. 2008..We propose that Rnr2-Rnr4 nuclear localization is achieved by a dynamic combination of Wtm1-mediated nuclear retention to limit export and regulated nuclear import through Dif1...
Research Grants
- Ribonucleotide Reductase: Structure and FunctionJoAnne Stubbe; Fiscal Year: 2010..The aim of this proposal is to study RNR's unique mechanism, the understanding of which will aid in developing novel RNR inhibitors. ..
- PURINE BIOSYNTHESIS ENZYMES-MECHANISMS AND REGULATIONJoAnne Stubbe; Fiscal Year: 2003..abstract_text> ..
- MECHANISM AND INHIBITION OF RIBONUCLEOTIDE REDUCTASESJoAnne Stubbe; Fiscal Year: 2001..Ultimately we would like to understand how the allosteric regulation of eucaryotic RNRs inside the cell control the fidelity of DNA replication, and the role of RNRs in check point control of the cell cycle. ..
- BIOSYNTHESIS OF PHAS, BIODEGRADABLE POLYMERSJoAnne Stubbe; Fiscal Year: 2001....
- BIOSYNTHESIS OF PHAS, BIODEGRADABLE POLYMERSJoAnne Stubbe; Fiscal Year: 2005....
- MECHANISM AND INHIBITION OF RIBONUCLEOTIDE REDUCTASESJoAnne Stubbe; Fiscal Year: 2005..cofactor is assembled in vivo is also being investigated. Understanding the regulation in yeast, with its many counterparts in humans, should lead to design of more effective therapeutics. ..
- Ribonucleotide Reductase Regulation: Diferric Y* assembly/maintenance and Sml1JoAnne Stubbe; Fiscal Year: 2009..Two regulatory mechanisms are examined in this proposal; understanding these mechanisms could lead to new therapeutic targets. ..
- Ribonucleotide Reductase Regulation: Diferric Y* assembly/maintenance and Sml1JoAnne Stubbe; Fiscal Year: 2010..Two regulatory mechanisms are examined in this proposal;understanding these mechanisms could lead to new therapeutic targets. ..
- Ribonucleotide Reductases: Structure and FunctionJoAnne Stubbe; Fiscal Year: 2009..The E. coli RNR and the S. cerevisiae and human RNRs are the focus of our efforts. ..
- Ribonucleotide Reductase Regulation: Diferric Y* assembly/maintenance and Sml1JoAnne Stubbe; Fiscal Year: 2009..Two regulatory mechanisms are examined in this proposal; understanding these mechanisms could lead to new therapeutic targets. ..
- Polyhydroxyalkanoates: A paradigm for non-template dependent polymerizationsJoAnne Stubbe; Fiscal Year: 2009..Understanding the roles of PhaC, PhaP and PhaZIa would be greatly enhanced with structural insight and efforts to crystallize proteins involved in PHB homeostasis will be actively pursued. ..
- Ribonucleotide Reductases: Structure and FunctionJoAnne Stubbe; Fiscal Year: 2007..The E. coli RNR and the S. cerevisiae and human RNRs are the focus of our efforts. ..
- Polyhydroxyalkanoates: A paradigm for non-template dependent polymerizationsJoAnne Stubbe; Fiscal Year: 2007..Understanding the roles of PhaC, PhaP and PhaZIa would be greatly enhanced with structural insight and efforts to crystallize proteins involved in PHB homeostasis will be actively pursued. ..
- MECHANISM OF DRUG INDUCED DNA DEGRADATIONJoAnne Stubbe; Fiscal Year: 2005..The structures of these lesions will be determined. The repair of these lesions by Apel will be investigated in an effort to determine its relevance to the non-homologous end joining ds-break repair. ..
- MECHANISM OF DRUG INDUCED DNA DEGRADATIONJoAnne Stubbe; Fiscal Year: 2000..Understanding resistance mechanisms can lead to rational removal of the resistance problem. ..
- MECHANISM OF DRUG-INDUCED DNA DEGRADATIONJoAnne Stubbe; Fiscal Year: 1993....
- PURINE BIOSYNTHETIC ENZYMES: MECHANISM & REGULATIONJoAnne Stubbe; Fiscal Year: 1993..Attempts will be made to define the function of purK gene product...
- PURINE BIOSYN ENZYMES:MECHANISM, INHIBITION, REGULATIONJoAnne Stubbe; Fiscal Year: 1990..New potent inhibitors of purine biosynthesis may be of use as chemotherapeutic agents and as aids in the investigation of the regulatory mechanisms involved in this pathway...