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1
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0035282866
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Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods
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Sofia H.J., Chen G., Hetzler B.G., Reyes-Spindola J.F., and Miller N.E. Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res 29 (2001) 1097-1106
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Nucleic Acids Res
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Sofia, H.J.1
Chen, G.2
Hetzler, B.G.3
Reyes-Spindola, J.F.4
Miller, N.E.5
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2
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39849096603
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The radical SAM superfamily
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This is the most current general review on the radical SAM superfamily, which discusses the biochemical activities and crystal structures for the radical SAM enzymes that have been characterized to date. This review presents the enzymes according to their reactivity with SAM, either as a cofactor or as a substrate.
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Frey P.A., Hegeman A.D., and Ruzicka F.J. The radical SAM superfamily. Crit Rev Biochem Mol Biol 43 (2008) 63-88. This is the most current general review on the radical SAM superfamily, which discusses the biochemical activities and crystal structures for the radical SAM enzymes that have been characterized to date. This review presents the enzymes according to their reactivity with SAM, either as a cofactor or as a substrate.
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(2008)
Crit Rev Biochem Mol Biol
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Frey, P.A.1
Hegeman, A.D.2
Ruzicka, F.J.3
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3
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13844275460
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Spectroscopic approaches to elucidating novel iron-sulfur chemistry in the 'Radical SAM' protein superfamily
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Walsby C., Ortillo D., Yang J., Nnyepi M., Broderick W.E., Hoffman B.M., and Broderick J.B. Spectroscopic approaches to elucidating novel iron-sulfur chemistry in the 'Radical SAM' protein superfamily. Inorg Chem 44 (2005) 727-741
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Inorg Chem
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Walsby, C.1
Ortillo, D.2
Yang, J.3
Nnyepi, M.4
Broderick, W.E.5
Hoffman, B.M.6
Broderick, J.B.7
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5
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0037174377
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An anchoring role for FeS Clusters: chelation of the amino acid moiety of S-adenosylmethionine to the unique iron site of the [4Fe-4S] cluster of pyruvate formate-lyase activating enzyme
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Walsby C.J., Ortillo D., Broderick W.E., Broderick J.B., and Hoffman B.M. An anchoring role for FeS Clusters: chelation of the amino acid moiety of S-adenosylmethionine to the unique iron site of the [4Fe-4S] cluster of pyruvate formate-lyase activating enzyme. J Am Chem Soc 124 (2002) 11270-11271
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J Am Chem Soc
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Walsby, C.J.1
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Broderick, W.E.3
Broderick, J.B.4
Hoffman, B.M.5
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6
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0141620318
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Coordination and mechanism of reversible cleavage of S-adenosylmethionine by the [4Fe-4S] center in lysine 2,3-aminomutase
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Chen D., Walsby C., Hoffman B.M., and Frey P.A. Coordination and mechanism of reversible cleavage of S-adenosylmethionine by the [4Fe-4S] center in lysine 2,3-aminomutase. J Am Chem Soc 125 (2003) 11788-11789
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Chen, D.1
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7
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0347504850
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Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes
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Layer G., Moser J., Heinz D.W., Jahn D., and Schubert W.-D. Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes. EMBO J 22 (2003) 6214-6224
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Layer, G.1
Moser, J.2
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Schubert, W.-D.5
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8
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0346727529
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Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme
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Berkovitch F., Nicolet Y., Wan J.T., Jarrett J.T., and Drennan C.L. Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science 303 (2004) 76-79
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Berkovitch, F.1
Nicolet, Y.2
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Drennan, C.L.5
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9
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4444346402
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Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans
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Hänzelmann P., and Schindelin H. Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans. Proc Natl Acad Sci U S A 101 (2004) 12870-12875
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Proc Natl Acad Sci U S A
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Hänzelmann, P.1
Schindelin, H.2
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10
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33646468635
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Binding of 5′-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism
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The crystal structure of MoaA with bound substrate, 5′-GTP, confirms residues involved with coordinating the substrate as well as offers insights into the ensuing radical reaction.
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Hänzelmann P., and Schindelin H. Binding of 5′-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism. Proc Natl Acad Sci U S A 103 (2006) 6829-6834. The crystal structure of MoaA with bound substrate, 5′-GTP, confirms residues involved with coordinating the substrate as well as offers insights into the ensuing radical reaction.
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Proc Natl Acad Sci U S A
, vol.103
, pp. 6829-6834
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Hänzelmann, P.1
Schindelin, H.2
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11
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25444494469
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The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale
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Lepore B.W., Ruzicka F.J., Frey P.A., and Ringe D. The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale. Proc Natl Acad Sci U S A 102 (2005) 13819-13824
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Proc Natl Acad Sci U S A
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Lepore, B.W.1
Ruzicka, F.J.2
Frey, P.A.3
Ringe, D.4
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12
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49649115936
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X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima
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Nicolet Y., Rubach J., Posewitz M., Amara P., Mathevon C., Atta M., Fontecave M., and Fontecilla-Camps J. X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima. J Biol Chem 283 (2008) 18861-18872
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J Biol Chem
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Nicolet, Y.1
Rubach, J.2
Posewitz, M.3
Amara, P.4
Mathevon, C.5
Atta, M.6
Fontecave, M.7
Fontecilla-Camps, J.8
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13
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55849139092
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Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme
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Providing the first structure of a radical SAM activase, this paper effectively demonstrates a structural basis for the direct and stereo-specific H-atom abstraction from PFL-AE's substrate, Gly734 of pyruvate formate-lyase.
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Vey J.L., Yang J., Li M., Broderick W.E., Broderick J.B., and Drennan C.L. Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme. Proc Natl Acad Sci U S A 105 (2008) 16137-16141. Providing the first structure of a radical SAM activase, this paper effectively demonstrates a structural basis for the direct and stereo-specific H-atom abstraction from PFL-AE's substrate, Gly734 of pyruvate formate-lyase.
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(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 16137-16141
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Vey, J.L.1
Yang, J.2
Li, M.3
Broderick, W.E.4
Broderick, J.B.5
Drennan, C.L.6
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14
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0034734328
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+ cluster of pyruvate formate-lyase activating enzyme generates the glycyl radical on pyruvate formate-lyase: EPR-detected single turnover
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+ cluster of pyruvate formate-lyase activating enzyme generates the glycyl radical on pyruvate formate-lyase: EPR-detected single turnover. J Am Chem Soc 122 (2000) 8331-8332
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J Am Chem Soc
, vol.122
, pp. 8331-8332
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Henshaw, T.F.1
Cheek, J.2
Broderick, J.B.3
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15
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0035805656
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2-,3- clusters with sulfonium cations: analogue reaction systems for the initial step in biotin synthase catalysis
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2-,3- clusters with sulfonium cations: analogue reaction systems for the initial step in biotin synthase catalysis. Inorg Chem 40 (2001) 2785-2793
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Inorg Chem
, vol.40
, pp. 2785-2793
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Daley, C.J.A.1
Holm, R.H.2
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16
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0141737459
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2,+ clusters with sulfonium cations: reactivity analogues of biotin synthase and other members of the S-adenosylmethionine enzyme family
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2,+ clusters with sulfonium cations: reactivity analogues of biotin synthase and other members of the S-adenosylmethionine enzyme family. J Inorg Biochem 97 (2003) 287-298
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(2003)
J Inorg Biochem
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, pp. 287-298
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Daley, C.J.A.1
Holm, R.H.2
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17
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0037432317
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Control of adenosylmethionine-dependent radical generation in biotin synthase: a kinetic and thermodynamic analysis of substrate binding to active and inactive forms of BioB
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Ugulava N., Frederick K.K., and Jarrett J.T. Control of adenosylmethionine-dependent radical generation in biotin synthase: a kinetic and thermodynamic analysis of substrate binding to active and inactive forms of BioB. Biochemistry 42 (2003) 2708-2719
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Biochemistry
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Ugulava, N.1
Frederick, K.K.2
Jarrett, J.T.3
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18
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33644860151
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Cofactor dependence of reduction potentials for [4Fe-4S]2+/1+ in lysine 2,3-aminomutase
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2+/1+ couple in the presence of AdoMet and other AdoMet analogs were measured by spectroelectrochemistry. This work shows that binding of AdoMet raises the reduction potential of the cluster giving reduction potentials in the midrange for ferrodoxin-like [4Fe-4S] clusters.
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2+/1+ couple in the presence of AdoMet and other AdoMet analogs were measured by spectroelectrochemistry. This work shows that binding of AdoMet raises the reduction potential of the cluster giving reduction potentials in the midrange for ferrodoxin-like [4Fe-4S] clusters.
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(2006)
Biochemistry
, vol.45
, pp. 3219-3225
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Hinckley, G.T.1
Frey, P.A.2
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19
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0035902569
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Biotin synthase contains two distinct iron-sulfur cluster binding sites: chemical and spectroelectrochemical analysis of iron-sulfur cluster interconversions
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Ugulava N.B., Gibney B.R., and Jarrett J.T. Biotin synthase contains two distinct iron-sulfur cluster binding sites: chemical and spectroelectrochemical analysis of iron-sulfur cluster interconversions. Biochemistry 40 (2001) 8343-8351
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Biochemistry
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, pp. 8343-8351
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Ugulava, N.B.1
Gibney, B.R.2
Jarrett, J.T.3
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20
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36048929198
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Binding energy in the one-electron reductive cleavage of S-adenosylmethionine in lysine 2,3-aminomutase, a radical SAM enzyme
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This work focuses on the importance of shifting of the binding energies in the active site of LAM in the presence of AdoMet and substrate in order to lower the energy barrier necessary for reductive cleavage of AdoMet.
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Wang S.C., and Frey P.A. Binding energy in the one-electron reductive cleavage of S-adenosylmethionine in lysine 2,3-aminomutase, a radical SAM enzyme. Biochemistry 46 (2007) 12889-12895. This work focuses on the importance of shifting of the binding energies in the active site of LAM in the presence of AdoMet and substrate in order to lower the energy barrier necessary for reductive cleavage of AdoMet.
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(2007)
Biochemistry
, vol.46
, pp. 12889-12895
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Wang, S.C.1
Frey, P.A.2
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21
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0035902555
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Spectroscopic changes during a single turnover of biotin synthase: destruction of a [2Fe-2S] cluster accompanies sulfur insertion
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Ugulava N.B., Sacanell C.J., and Jarrett J.T. Spectroscopic changes during a single turnover of biotin synthase: destruction of a [2Fe-2S] cluster accompanies sulfur insertion. Biochemistry 40 (2001) 8352-8358
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Biochemistry
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Ugulava, N.B.1
Sacanell, C.J.2
Jarrett, J.T.3
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23
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33746918356
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How an enzyme tames reactive intermediates: positioning of the active-site components of lysine 2,3-aminomutase during enzymatic turnover as determined by ENDOR spectroscopy
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Using ENDOR to probe the active site of LAM, this group was able to monitor the interactions of the components involved in catalysis to further discern how an enzyme controls radical intermediates.
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Lees N.S., Chen D., Walsby C., Behshad E., Frey P.A., and Hoffman B.M. How an enzyme tames reactive intermediates: positioning of the active-site components of lysine 2,3-aminomutase during enzymatic turnover as determined by ENDOR spectroscopy. J Am Chem Soc 128 (2006) 10145-10154. Using ENDOR to probe the active site of LAM, this group was able to monitor the interactions of the components involved in catalysis to further discern how an enzyme controls radical intermediates.
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J Am Chem Soc
, vol.128
, pp. 10145-10154
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Lees, N.S.1
Chen, D.2
Walsby, C.3
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Frey, P.A.5
Hoffman, B.M.6
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24
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0032748442
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Spectroscopic evidence for the participation of an allylic analogue of the 5′-deoxyadenosyl radical in the reaction of lysine 2,3-aminomutase
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Magnusson O.T., Reed G.H., and Frey P.A. Spectroscopic evidence for the participation of an allylic analogue of the 5′-deoxyadenosyl radical in the reaction of lysine 2,3-aminomutase. J Am Chem Soc 121 (1999) 9764-9765
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Characterization of an allylic analogue of the 5′-deoxyadenosyl radical: an intermediate in the reaction of lysine 2,3-aminomutase
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Magnusson O.T., Reed G.H., and Frey P.A. Characterization of an allylic analogue of the 5′-deoxyadenosyl radical: an intermediate in the reaction of lysine 2,3-aminomutase. Biochemistry 40 (2001) 7773-7782
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Magnusson, O.T.1
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Activation of the anaerobic ribonucleotide reductase from Escherichia coli. The essential role of the iron-sulfur center for S-adenosylmethionine reduction
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Ollagnier S., Mulliez E., Schmidt P.P., Eliasson R., Gaillard J., Deronzier C., Bergman T., Gräslund A., Reichard P., and Fontecave M. Activation of the anaerobic ribonucleotide reductase from Escherichia coli. The essential role of the iron-sulfur center for S-adenosylmethionine reduction. J Biol Chem 272 (1997) 24216-24223
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Ollagnier, S.1
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Bergman, T.7
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0035957239
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Activation of class III ribonucleotide reductase by flavodoxin: a protein radical-driven electron transfer to the iron-sulfur center
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Mulliez E., Padovani D., Atta M., Alcouffe C., and Fontecave M. Activation of class III ribonucleotide reductase by flavodoxin: a protein radical-driven electron transfer to the iron-sulfur center. Biochemistry 40 (2001) 3730-3736
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61349164311
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DNA repair and free radicals, new insights into the mechanism of spore photoproduct lyase revealed by single amino acid substitution
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Chandor-Proust A., Berteau O., Douki T., Gasparutto D., Ollagnier-de-Choudens S., Fontecave M., and Atta M. DNA repair and free radicals, new insights into the mechanism of spore photoproduct lyase revealed by single amino acid substitution. J Biol Chem 283 (2008) 36361-36368
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Chandor-Proust, A.1
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The subunit structure and catalytic mechanism of the Bacillus subtilis DNA repair enzyme spore photoproduct lyase
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Rebeil R., and Nicholson W.L. The subunit structure and catalytic mechanism of the Bacillus subtilis DNA repair enzyme spore photoproduct lyase. Proc Natl Acad Sci U S A 98 (2001) 9038-9043
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Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrate
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Pieck J.C., Hennecke U., Pierik A.J., Friedel M.G., and Carell T. Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrate. J Biol Chem 281 (2006) 36317-36326
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Radical S-adenosylmethionine enzyme coproporphyrinogen III oxidase HemN: functional features of the [4Fe-4S] cluster and the two bound S-adenosyl-L-methionines
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Layer G., Grage K., Teschner T., Schunemann V., Breckau D., Masoumi A., Jahn M., Heathcote P., Trautwein A., and Jahn D. Radical S-adenosylmethionine enzyme coproporphyrinogen III oxidase HemN: functional features of the [4Fe-4S] cluster and the two bound S-adenosyl-L-methionines. J Biol Chem 280 (2005) 29038-29046
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