PERRY FREY

Summary

Affiliation: University of Wisconsin
Country: USA

Publications

  1. doi request reprint Advances in research on metalloproteins
    Perry A Frey
    Department of Biochemistry, Institute for Enzyme Research, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI, 53706, USA
    Methods Mol Biol 1122:1-3. 2014
  2. doi request reprint Chemical and stereochemical actions of UDP-galactose 4-epimerase
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53705, USA
    Acc Chem Res 46:1417-26. 2013
  3. ncbi request reprint The ubiquity of iron
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53726, USA
    ACS Chem Biol 7:1477-81. 2012
  4. doi request reprint Pyridoxal-5'-phosphate as the catalyst for radical isomerization in reactions of PLP-dependent aminomutases
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53726, USA
    Biochim Biophys Acta 1814:1548-57. 2011
  5. ncbi request reprint The Radical SAM Superfamily
    Perry A Frey
    Department of Biochemistry, University of Madison, Wisconin Madison, Wisconsin 53726, USA
    Crit Rev Biochem Mol Biol 43:63-88. 2008
  6. ncbi request reprint Radical mechanisms in adenosylmethionine- and adenosylcobalamin-dependent enzymatic reactions
    P A Frey
    Department of Biochemistry, University of Wisconsin Madison 53705, USA
    Arch Biochem Biophys 382:6-14. 2000
  7. ncbi request reprint S-Adenosylmethionine: a wolf in sheep's clothing, or a rich man's adenosylcobalamin?
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53726, USA
    Chem Rev 103:2129-48. 2003
  8. ncbi request reprint Radical mechanisms of enzymatic catalysis
    P A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53705, USA
    Annu Rev Biochem 70:121-48. 2001
  9. ncbi request reprint The role of radicals in enzymatic processes
    P A Frey
    Department of Biochemistry, University of Wisconsin Madison, 53705, USA
    Chem Rec 1:277-89. 2001
  10. ncbi request reprint S-adenosylmethionine as an oxidant: the radical SAM superfamily
    Susan C Wang
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53726, USA
    Trends Biochem Sci 32:101-10. 2007

Research Grants

  1. MECHANISMS OF ENZYMATIC REACTIONS
    PERRY FREY; Fiscal Year: 1993
  2. ENZYME CATALYSIS OF ELECTRON AND GROUP TRANSFER
    PERRY FREY; Fiscal Year: 2002
  3. ENZYME CATALYSIS OF ELECTRON AND GROUP TRANSFER
    PERRY FREY; Fiscal Year: 2006
  4. MECHANISMS OF ENZYMATIC REACTIONS
    PERRY FREY; Fiscal Year: 2002
  5. MECHANISMS OF ENZYMATIC REACTIONS
    PERRY FREY; Fiscal Year: 1990
  6. ENZYME CATALYSIS OF ELECTRON AND GROUP TRANSFER
    PERRY FREY; Fiscal Year: 1990
  7. MECHANISMS OF ENZYMATIC REACTIONS
    PERRY FREY; Fiscal Year: 2006

Collaborators

  • George H Reed
  • G G Petsko
  • Brian Hoffman
  • G Michael Blackburn
  • CATHERINE DRENNAN
  • Dawei Chen
  • Phillip A Schwartz
  • Kuo Hsiang Tang
  • Frank J Ruzicka
  • Susan C Wang
  • Olafur Th Magnusson
  • Glen T Hinckley
  • Kaisheng Huang
  • Steven O Mansoorabadi
  • Bryan W Lepore
  • Dagmar Ringe
  • Abolfazl Arabshahi
  • Jason G McCoy
  • Nicholas S Lees
  • Elham Behshad
  • Frederick Berkovitch
  • Jane A Beebe
  • Jeffrey W Gross
  • Sandaruwan Geeganage
  • Russell Lobrutto
  • Justinn Tanem
  • Charles J Walsby
  • Eduard Bitto
  • Craig A Bingman
  • Russell R Poyner
  • George N Phillips
  • Eva A Enns
  • Yaoming Wei
  • Weiming Wu
  • James G Clifton
  • Charles Walsby
  • Anthony D Casarez
  • Mark J Thompson
  • Amy Harms

Detail Information

Publications38

  1. doi request reprint Advances in research on metalloproteins
    Perry A Frey
    Department of Biochemistry, Institute for Enzyme Research, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI, 53706, USA
    Methods Mol Biol 1122:1-3. 2014
    ..They also facilitate many one-electron chemical reactions involving free radical intermediates. Iron, being the dominant element in the earth and a transition metal, most frequently participates in biological one-electron chemistry. ..
  2. doi request reprint Chemical and stereochemical actions of UDP-galactose 4-epimerase
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53705, USA
    Acc Chem Res 46:1417-26. 2013
    ..In an O₂-dependent reaction, [GalE-NADH] reduces the stable radical UDP-TEMPO with production of superoxide radical. The reaction must proceed by way of a NAD-pyridinyl radical intermediate...
  3. ncbi request reprint The ubiquity of iron
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53726, USA
    ACS Chem Biol 7:1477-81. 2012
    ..It seems likely that other solid planets, formed by the same processes as Earth, would also foster the evolution of life and that iron would be similarly important to life on those planets as it is on Earth...
  4. doi request reprint Pyridoxal-5'-phosphate as the catalyst for radical isomerization in reactions of PLP-dependent aminomutases
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53726, USA
    Biochim Biophys Acta 1814:1548-57. 2011
    ..This article is part of a Special Issue entitled: Pyridoxal Phospate Enzymology...
  5. ncbi request reprint The Radical SAM Superfamily
    Perry A Frey
    Department of Biochemistry, University of Madison, Wisconin Madison, Wisconsin 53726, USA
    Crit Rev Biochem Mol Biol 43:63-88. 2008
    ....
  6. ncbi request reprint Radical mechanisms in adenosylmethionine- and adenosylcobalamin-dependent enzymatic reactions
    P A Frey
    Department of Biochemistry, University of Wisconsin Madison 53705, USA
    Arch Biochem Biophys 382:6-14. 2000
    ..The mechanism by which AdoMet is cleaved to the 5'-deoxyadenosyl radical at enzymatic sites will also be discussed...
  7. ncbi request reprint S-Adenosylmethionine: a wolf in sheep's clothing, or a rich man's adenosylcobalamin?
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53726, USA
    Chem Rev 103:2129-48. 2003
  8. ncbi request reprint Radical mechanisms of enzymatic catalysis
    P A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53705, USA
    Annu Rev Biochem 70:121-48. 2001
    ..Three examples are described of suicide inactivation through the formation of exceptionally stable free radicals at enzymatic active sites...
  9. ncbi request reprint The role of radicals in enzymatic processes
    P A Frey
    Department of Biochemistry, University of Wisconsin Madison, 53705, USA
    Chem Rec 1:277-89. 2001
    ..The cis-ethanesemidione radical has been characterized by EPR spectroscopy. Its exceptional stability at the active site is the basis for the inactivation of DDH by glycolaldehyde...
  10. ncbi request reprint S-adenosylmethionine as an oxidant: the radical SAM superfamily
    Susan C Wang
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53726, USA
    Trends Biochem Sci 32:101-10. 2007
    ..Recent results are beginning to determine the unique biochemistry for some of the radical SAM enzymes, for example, lysine 2,3 aminomutase, pyruvate formate lyase activase and biotin synthase...
  11. ncbi request reprint Free radical mechanisms in enzymology
    Perry A Frey
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Chem Rev 106:3302-16. 2006
  12. ncbi request reprint Kinetic characterization of transient free radical intermediates in reaction of lysine 2,3-aminomutase by EPR lineshape analysis
    Perry A Frey
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53726, USA
    Methods Enzymol 354:426-35. 2002
  13. pmc Analysis of the Cob(II)alamin-5'-deoxy-3',4'-anhydroadenosyl radical triplet spin system in the active site of diol dehydrase
    Steven O Mansoorabadi
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53726 4087, USA
    Biochemistry 45:14362-70. 2006
    ..Homolytic cleavage of the cobalt-carbon bond of the analogue in the absence of the substrate indicates that, in diol dehydrase, binding of the coenzyme to the protein weakens the bond prior to binding of the substrate...
  14. pmc Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana
    Jason G McCoy
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Biochemistry 45:3154-62. 2006
    ..The value of K(eq) in the direction of ADP and glucose-1-P formation is 5.0 at pH 7.0 and 25 degrees C in the absence of a divalent metal ion, and it is 40 in the presence of 1 mM MgCl(2)...
  15. pmc The x-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale
    Bryan W Lepore
    Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, 1710 University Avenue, Madison, WI 53726, USA
    Proc Natl Acad Sci U S A 102:13819-24. 2005
    ..The chain fold in the central domain is in part analogous to other radical-SAM enzymes...
  16. pmc Probing interactions from solvent-exchangeable protons and monovalent cations with the 1,2-propanediol-1-yl radical intermediate in the reaction of dioldehydrase
    Phillip A Schwartz
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53726, USA
    Protein Sci 16:1157-64. 2007
    ..The spectroscopic evidence did not implicate a direct coordination of the activating cation and the substrate derived radical intermediate...
  17. pmc Radical triplets and suicide inhibition in reactions of 4-thia-D- and 4-thia-L-lysine with lysine 5,6-aminomutase
    Kuo Hsiang Tang
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Biochemistry 48:8151-60. 2009
    ..The observation of the transient radical supports the hypothetical isomerization mechanism...
  18. pmc 5'-Peroxyadenosine and 5'-peroxyadenosylcobalamin as intermediates in the aerobic photolysis of adenosylcobalamin
    Phillip A Schwartz
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Biochemistry 46:7284-92. 2007
    ....
  19. pmc Binding energy in the one-electron reductive cleavage of S-adenosylmethionine in lysine 2,3-aminomutase, a radical SAM enzyme
    Susan C Wang
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Biochemistry 46:12889-95. 2007
    ....
  20. ncbi request reprint Facile hydrogen-deuterium exchange at the 5'-position of an analogue of S-adenosyl-l-methionine
    Olafur Th Magnusson
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, 53705, USA
    Bioorg Chem 30:53-61. 2002
    ..Solvent exchange under these mild conditions provides a simple way to prepare a 5'-2H-labeled form of the coenzyme analogue...
  21. pmc Glutamate 2,3-aminomutase: a new member of the radical SAM superfamily of enzymes
    Frank J Ruzicka
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53726, USA
    Biochim Biophys Acta 1774:286-96. 2007
    ..difficile is a representative of a family found in a number of bacteria. It is likely that the beta-glutamate found in a few bacterial and archeal species as an osmolyte arises from the action of glutamate 2,3-aminomutase...
  22. pmc Identification of structural and catalytic classes of highly conserved amino acid residues in lysine 2,3-aminomutase
    Dawei Chen
    Department of Biochemistry, University of Wisconsin, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Biochemistry 45:12647-53. 2006
    ..In particular, a network of hydrogen bonded interactions of Arg130, Glu86, Arg135, and the main chain carbonyl groups of Cys132 and Leu55 appears to stabilize the [4Fe-4S] cluster...
  23. pmc Cofactor dependence of reduction potentials for [4Fe-4S]2+/1+ in lysine 2,3-aminomutase
    Glen T Hinckley
    Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Biochemistry 45:3219-25. 2006
    ..The energetic barrier in the reductive cleavage of SAM may be overcome through the use of binding energy...
  24. ncbi request reprint Adenosyl coenzyme and pH dependence of the [4Fe-4S]2+/1+ transition in lysine 2,3-aminomutase
    Glen T Hinckley
    Department of Biochemistry, University of Wisconsin Madison, 53705, USA
    Arch Biochem Biophys 414:34-9. 2003
    ..These features are also absent in the spectra at all pHs examined when reduction is induced by azaSAM or SAH...
  25. ncbi request reprint Identification of a novel pyridoxal 5'-phosphate binding site in adenosylcobalamin-dependent lysine 5,6-aminomutase from Porphyromonas gingivalis
    Kuo Hsiang Tang
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Biochemistry 41:8767-76. 2002
    ..In summary, we introduce a novel PLP-binding motif, the first to be discovered in an AdoCbl-dependent enzyme...
  26. ncbi request reprint Coordination and mechanism of reversible cleavage of S-adenosylmethionine by the [4Fe-4S] center in lysine 2,3-aminomutase
    Dawei Chen
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    J Am Chem Soc 125:11788-9. 2003
    ....
  27. ncbi request reprint Kinetic and biochemical analysis of the mechanism of action of lysine 5,6-aminomutase
    Kuo Hsiang Tang
    Department of Biochemistry, University of Wisconsin Madison, 53726, USA
    Arch Biochem Biophys 418:49-54. 2003
    ..The putative substrate-related radical intermediate is not sufficiently stabilized by the nonbonding 4-oxa electrons to be detectable by EPR spectroscopy...
  28. ncbi request reprint Interactions of diol dehydrase and 3',4'-anhydroadenosylcobalamin: suicide inactivation by electron transfer
    Olafur Th Magnusson
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53705, USA
    Biochemistry 41:1695-702. 2002
    ..This study provides an example of suicide inactivation of a radical enzyme brought about by a side reaction of an analogue of the radical intermediate...
  29. pmc Dioldehydrase: an essential role for potassium ion in the homolytic cleavage of the cobalt-carbon bond in adenosylcobalamin
    Phillip A Schwartz
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Biochemistry 46:7293-301. 2007
    ..The results indicate that dioldehydrase likely harvests the binding energy of the activating monocation to stimulate the homolytic cleavage of the Co-C5' bond in adenosylcobalamin...
  30. ncbi request reprint Engineering human Fhit, a diadenosine triphosphate hydrolase, into an efficient dinucleoside polyphosphate synthase
    Kaisheng Huang
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    J Am Chem Soc 126:9548-9. 2004
    ..We here describe the use of H96G-Fhit to catalyze the synthesis of Ap3A, Ap3C, Ap3G, Ap3T, Ap3U, Cp3U, Tp3U, dAp3U, Ap4A, Ap4U, and the fluorescent Ap4etheno-C...
  31. pmc Basis for the equilibrium constant in the interconversion of l-lysine and l-beta-lysine by lysine 2,3-aminomutase
    Dawei Chen
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, WI 53726, USA
    Biochim Biophys Acta 1774:297-302. 2007
    ..4 kcal mol(-1) and DeltaS degrees =-0.25 cal deg(-1) mol(-1). Exothermicity is attributed to the greater strength of the bond C(beta)-N(beta) in l-beta-lysine than C(alpha)-N(alpha) in l-lysine, and this should hold for other amino acids...
  32. ncbi request reprint Galactose mutarotase: pH dependence of enzymatic mutarotation
    Jane A Beebe
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Biochemistry 42:4414-20. 2003
    ..8 for H104Q and 6.3 for E309Q. Apparently, ring opening of alpha-D-glucose limits the rate at low pHs, but ring closure does not become rate limiting at pHs up to 8.5 in reactions of these variants...
  33. ncbi request reprint The mechanism of action of the fragile histidine triad, Fhit: isolation of a covalent adenylyl enzyme and chemical rescue of H96G-Fhit
    Kaisheng Huang
    Department of Biochemistry, University of Wisconsin Madison, 1710 University Avenue, Madison, Wisconsin 53726, USA
    Biochemistry 43:7637-42. 2004
    ..The results indicate that Mg(2+) in the reaction of Ap(3)A is required for the first step, the formation of the covalent intermediate Fhit-AMP, and not for the hydrolysis of the intermediate in the second step...
  34. pmc A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase
    Frederick Berkovitch
    Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 101:15870-5. 2004
    ..Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate...
  35. ncbi request reprint Rapid mix-quench MALDI-TOF mass spectrometry for analysis of enzymatic systems
    Jeffrey W Gross
    GlaxoSmith Kline, King of Prussia, Pennsylvania 19406, USA
    Methods Enzymol 354:27-49. 2002
  36. ncbi request reprint 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
    Nicholas S Lees
    Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
    J Am Chem Soc 128:10145-54. 2006
    ..This constraint enables the enzyme to minimize and even eliminate side reactions of highly reactive species such as the 5'-deoxyadensosyl radical...
  37. ncbi request reprint Snapshots of three intermediates at the active site of pyruvate oxidase
    Perry A Frey
    Nat Chem Biol 2:294-5. 2006
  38. ncbi request reprint Galactose-1-phosphate uridylyltransferase: kinetics of formation and reaction of uridylyl-enzyme intermediate in wild-type and specifically mutated uridylyltransferases
    Sandaruwan Geeganage
    Cancer Research Division, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
    Methods Enzymol 354:134-48. 2002

Research Grants40

  1. MECHANISMS OF ENZYMATIC REACTIONS
    PERRY FREY; Fiscal Year: 1993
    ....
  2. ENZYME CATALYSIS OF ELECTRON AND GROUP TRANSFER
    PERRY FREY; Fiscal Year: 2002
    ..If the beta-aminoacyl substituents function in this way, they could become significant in drug delivery strategies, especially for candidate drugs that are minimally soluble. ..
  3. ENZYME CATALYSIS OF ELECTRON AND GROUP TRANSFER
    PERRY FREY; Fiscal Year: 2006
    ..The contributions of beta- amino acids produced by lysine 2,3-aminomutase and arginine 2,3-aminomutase to the functions of antibiotics are not known. The beta-aminoacids may become significant in drug development. ..
  4. MECHANISMS OF ENZYMATIC REACTIONS
    PERRY FREY; Fiscal Year: 2002
    ..Crystallization trials will be pursued with the objective of determining the first structured in the Ga1K family of sugar phosphotransferases. ..
  5. MECHANISMS OF ENZYMATIC REACTIONS
    PERRY FREY; Fiscal Year: 1990
    ..Specific chemical modification using affinity labeling agents and radio-chemically labeled substrates will be applied, as well as site-directed mutagenesis. The catalytic roles of these functional groups will be rigorously defined...
  6. ENZYME CATALYSIS OF ELECTRON AND GROUP TRANSFER
    PERRY FREY; Fiscal Year: 1990
    ..The reaction mechanism will be investigated by determining the tritium-kinetic isotope effect for the reaction of beta-[2-3H]lysine. The involvement of pridoxal phospate in this B12-like reaction will also be investigated...
  7. MECHANISMS OF ENZYMATIC REACTIONS
    PERRY FREY; Fiscal Year: 2006
    ..Research on Fhit is directed toward elucidating its chemical reaction mechanism and the chemical basis for its activity as a tumor suppressor and its mechanistic relationships with galactose-1-P uridylyltransferase. ..