Phoebe A. Rice - Publications

Affiliations: 
Biochemistry and Molecular Biology University of Chicago, Chicago, IL 
Area:
Structural biochemistry of DNA recombination
Website:
http://biophysics.uchicago.edu/the-faculty/phoebe_rice/

68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Mir-Sanchis I, Roman CA, Misiura A, Pigli YZ, Boyle-Vavra S, Rice PA. Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative. Nature Structural & Molecular Biology. PMID 27571176 DOI: 10.1038/Nsmb.3286  1
2015 Suslov NB, DasGupta S, Huang H, Fuller JR, Lilley DM, Rice PA, Piccirilli JA. Crystal structure of the Varkud satellite ribozyme. Nature Chemical Biology. 11: 840-6. PMID 26414446 DOI: 10.1038/Nchembio.1929  1
2015 Rice PA. Serine Resolvases. Microbiology Spectrum. 3: MDNA3-0045-2014. PMID 26104713 DOI: 10.1128/microbiolspec.MDNA3-0045-2014  1
2015 Ling L, Montaño SP, Sauer RT, Rice PA, Baker TA. Deciphering the Roles of Multicomponent Recognition Signals by the AAA+ Unfoldase ClpX. Journal of Molecular Biology. 427: 2966-82. PMID 25797169 DOI: 10.1016/J.Jmb.2015.03.008  1
2014 Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nature Chemical Biology. 10: 686-91. PMID 24952597 DOI: 10.1038/Nchembio.1561  1
2013 Boocock MR, Rice PA. A proposed mechanism for IS607-family serine transposases. Mobile Dna. 4: 24. PMID 24195768 DOI: 10.1186/1759-8753-4-24  1
2013 Vivas P, Velmurugu Y, Kuznetsov SV, Rice PA, Ansari A. Global analysis of ion dependence unveils hidden steps in DNA binding and bending by integration host factor. The Journal of Chemical Physics. 139: 121927. PMID 24089739 DOI: 10.1063/1.4818596  1
2013 Keenholtz RA, Mouw KW, Boocock MR, Li NS, Piccirilli JA, Rice PA. Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage. The Journal of Biological Chemistry. 288: 29206-14. PMID 23970547 DOI: 10.1074/Jbc.M113.508028  1
2013 Misiura A, Pigli YZ, Boyle-Vavra S, Daum RS, Boocock MR, Rice PA. Roles of two large serine recombinases in mobilizing the methicillin-resistance cassette SCCmec. Molecular Microbiology. 88: 1218-29. PMID 23651464 DOI: 10.1111/Mmi.12253  1
2012 Montaño SP, Pigli YZ, Rice PA. The μ transpososome structure sheds light on DDE recombinase evolution. Nature. 491: 413-7. PMID 23135398 DOI: 10.1038/Nature11602  1
2012 Vivas P, Velmurugu Y, Kuznetsov SV, Rice PA, Ansari A. Mapping the transition state for DNA bending by IHF. Journal of Molecular Biology. 418: 300-15. PMID 22370561 DOI: 10.1016/J.Jmb.2012.02.028  1
2011 Haddadian EJ, Gong H, Jha AK, Yang X, Debartolo J, Hinshaw JR, Rice PA, Sosnick TR, Freed KF. Automated real-space refinement of protein structures using a realistic backbone move set. Biophysical Journal. 101: 899-909. PMID 21843481 DOI: 10.1016/J.Bpj.2011.06.063  1
2011 Flott S, Kwon Y, Pigli YZ, Rice PA, Sung P, Jackson SP. Regulation of Rad51 function by phosphorylation. Embo Reports. 12: 833-9. PMID 21738226 DOI: 10.1038/Embor.2011.127  1
2011 Keenholtz RA, Rowland SJ, Boocock MR, Stark WM, Rice PA. Structural basis for catalytic activation of a serine recombinase. Structure (London, England : 1993). 19: 799-809. PMID 21645851 DOI: 10.1016/J.Str.2011.03.017  1
2011 Montaño SP, Rice PA. Moving DNA around: DNA transposition and retroviral integration. Current Opinion in Structural Biology. 21: 370-8. PMID 21439812 DOI: 10.1016/J.Sbi.2011.03.004  1
2010 Mouw KW, Steiner AM, Ghirlando R, Li NS, Rowland SJ, Boocock MR, Stark WM, Piccirilli JA, Rice PA. Sin resolvase catalytic activity and oligomerization state are tightly coupled. Journal of Molecular Biology. 404: 16-33. PMID 20868695 DOI: 10.1016/J.Jmb.2010.08.057  1
2010 Chaconas G, Craig N, Curcio MJ, Deininger P, Feschotte C, Levin H, Rice PA, Voytas DF. Meeting report for mobile DNA 2010. Mobile Dna. 1: 20. PMID 20735816 DOI: 10.1186/1759-8753-1-20  1
2010 Zhang AP, Pigli YZ, Rice PA. Structure of the LexA-DNA complex and implications for SOS box measurement. Nature. 466: 883-6. PMID 20703307 DOI: 10.1038/Nature09200  1
2010 Rice PA, Mouw KW, Montaño SP, Boocock MR, Rowland SJ, Stark WM. Orchestrating serine resolvases. Biochemical Society Transactions. 38: 384-7. PMID 20298188 DOI: 10.1042/Bst0380384  1
2009 Poor CB, Chen PR, Duguid E, Rice PA, He C. Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus. The Journal of Biological Chemistry. 284: 23517-24. PMID 19586910 DOI: 10.1074/Jbc.M109.015826  1
2009 Rowland SJ, Boocock MR, McPherson AL, Mouw KW, Rice PA, Stark WM. Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome. Molecular Microbiology. 74: 282-98. PMID 19508283 DOI: 10.1111/J.1365-2958.2009.06756.X  1
2009 Grigorescu AA, Vissers JH, Ristic D, Pigli YZ, Lynch TW, Wyman C, Rice PA. Inter-subunit interactions that coordinate Rad51's activities. Nucleic Acids Research. 37: 557-67. PMID 19066203 DOI: 10.1093/Nar/Gkn973  1
2008 Peng X, Pigli YZ, Rice PA, Greenberg MM. Protein binding has a large effect on radical mediated DNA damage. Journal of the American Chemical Society. 130: 12890-1. PMID 18778053 DOI: 10.1021/Ja805440V  1
2008 Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA. Architecture of a serine recombinase-DNA regulatory complex. Molecular Cell. 30: 145-55. PMID 18439894 DOI: 10.1016/J.Molcel.2008.02.023  1
2008 Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature. 452: 961-5. PMID 18432238 DOI: 10.1038/Nature06889  1
2008 Whiteson KL, Rice PA. Binding and catalytic contributions to site recognition by flp recombinase. The Journal of Biological Chemistry. 283: 11414-23. PMID 18276592 DOI: 10.1074/Jbc.M800106200  1
2007 Mizuuchi M, Rice PA, Wardle SJ, Haniford DB, Mizuuchi K. Control of transposase activity within a transpososome by the configuration of the flanking DNA segment of the transposon. Proceedings of the National Academy of Sciences of the United States of America. 104: 14622-7. PMID 17785414 DOI: 10.1073/Pnas.0706556104  1
2007 Whiteson KL, Chen Y, Chopra N, Raymond AC, Rice PA. Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305. Chemistry & Biology. 14: 121-9. PMID 17317566 DOI: 10.1016/J.Chembiol.2007.01.011  1
2007 Mouw KW, Rice PA. Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb. Molecular Microbiology. 63: 1319-30. PMID 17244195 DOI: 10.1111/J.1365-2958.2007.05586.X  1
2007 Swinger KK, Rice PA. Structure-based analysis of HU-DNA binding. Journal of Molecular Biology. 365: 1005-16. PMID 17097674 DOI: 10.1016/J.Jmb.2006.10.024  1
2006 Khrapunov S, Brenowitz M, Rice PA, Catalano CE. Binding then bending: a mechanism for wrapping DNA. Proceedings of the National Academy of Sciences of the United States of America. 103: 19217-8. PMID 17159146 DOI: 10.1073/Pnas.0609223103  1
2006 Lu CP, Sandoval H, Brandt VL, Rice PA, Roth DB. Amino acid residues in Rag1 crucial for DNA hairpin formation. Nature Structural & Molecular Biology. 13: 1010-5. PMID 17028591 DOI: 10.1038/Nsmb1154  1
2006 Chen PR, Bae T, Williams WA, Duguid EM, Rice PA, Schneewind O, He C. An oxidation-sensing mechanism is used by the global regulator MgrA in Staphylococcus aureus. Nature Chemical Biology. 2: 591-5. PMID 16980961 DOI: 10.1038/Nchembio820  1
2006 Grindley ND, Whiteson KL, Rice PA. Mechanisms of site-specific recombination. Annual Review of Biochemistry. 75: 567-605. PMID 16756503 DOI: 10.1146/Annurev.Biochem.73.011303.073908  1
2005 Rice PA. Resolving integral questions in site-specific recombination. Nature Structural & Molecular Biology. 12: 641-3. PMID 16077726 DOI: 10.1038/Nsmb0805-641  1
2005 Duguid EM, Rice PA, He C. The structure of the human AGT protein bound to DNA and its implications for damage detection. Journal of Molecular Biology. 350: 657-66. PMID 15964013 DOI: 10.1016/J.Jmb.2005.05.028  1
2005 Rice PA. Visualizing Mu transposition: assembling the puzzle pieces. Genes & Development. 19: 773-5. PMID 15805467 DOI: 10.1101/Gad.1309305  1
2004 Conway AB, Lynch TW, Zhang Y, Fortin GS, Fung CW, Symington LS, Rice PA. Crystal structure of a Rad51 filament. Nature Structural & Molecular Biology. 11: 791-6. PMID 15235592 DOI: 10.1038/Nsmb795  1
2004 Swinger KK, Rice PA. IHF and HU: flexible architects of bent DNA. Current Opinion in Structural Biology. 14: 28-35. PMID 15102446 DOI: 10.1016/J.Sbi.2003.12.003  1
2003 Swinger KK, Lemberg KM, Zhang Y, Rice PA. Flexible DNA bending in HU-DNA cocrystal structures. The Embo Journal. 22: 3749-60. PMID 12853489 DOI: 10.1093/Emboj/Cdg351  1
2003 Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA. Integration host factor: putting a twist on protein-DNA recognition. Journal of Molecular Biology. 330: 493-502. PMID 12842466 DOI: 10.1016/S0022-2836(03)00529-1  1
2003 Chen Y, Rice PA. The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis. The Journal of Biological Chemistry. 278: 24800-7. PMID 12716882 DOI: 10.1074/Jbc.M300853200  1
2003 Chen Y, Rice PA. New insight into site-specific recombination from Flp recombinase-DNA structures. Annual Review of Biophysics and Biomolecular Structure. 32: 135-59. PMID 12598365 DOI: 10.1146/Annurev.Biophys.32.110601.141732  1
2003 Conway AB, Chen Y, Rice PA. Structural plasticity of the Flp-Holliday junction complex. Journal of Molecular Biology. 326: 425-34. PMID 12559911 DOI: 10.1016/S0022-2836(02)01370-0  1
2001 Rice PA, Baker TA. Comparative architecture of transposase and integrase complexes. Nature Structural Biology. 8: 302-7. PMID 11774877 DOI: 10.1038/86166  1
2001 Drum CL, Shen Y, Rice PA, Bohm A, Tang WJ. Crystallization and preliminary X-ray study of the edema factor exotoxin adenylyl cyclase domain from Bacillus anthracis in the presence of its activator, calmodulin. Acta Crystallographica. Section D, Biological Crystallography. 57: 1881-4. PMID 11717504 DOI: 10.1107/S0907444901014937  1
2000 Chen Y, Narendra U, Iype LE, Cox MM, Rice PA. Crystal structure of a Flp recombinase-holliday junction complex: Assembly of an active oligomer by helix swapping Molecular Cell. 6: 885-897. PMID 11090626 DOI: 10.1016/S1097-2765(00)00086-1  1
1999 Rice PA. Holding damaged DNA together Nature Structural Biology. 6: 805-806. PMID 10467087 DOI: 10.1038/12257  1
1997 Rice PA. Making DNA do a U-turn: IHF and related proteins Current Opinion in Structural Biology. 7: 86-93. PMID 9032059 DOI: 10.1016/S0959-440X(97)80011-5  1
1996 Rice PA, Yang S, Mizuuchi K, Nash HA. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell. 87: 1295-306. PMID 8980235 DOI: 10.1016/S0092-8674(00)81824-3  1
1996 Rice P, Craigie R, Davies DR. Retroviral integrases and their cousins Current Opinion in Structural Biology. 6: 76-83. PMID 8696976 DOI: 10.1016/S0959-440X(96)80098-4  1
1995 Rice P, Mizuuchi K. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell. 82: 209-20. PMID 7628012 DOI: 10.1016/0092-8674(95)90308-9  1
1995 Savilahti H, Rice PA, Mizuuchi K. The phage Mu transpososome core: DNA requirements for assembly and function. The Embo Journal. 14: 4893-903. PMID 7588618 DOI: 10.1002/J.1460-2075.1995.Tb00170.X  1
1994 Rice PA, Steitz TA. Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits. The Embo Journal. 13: 1514-24. PMID 8156989 DOI: 10.2210/Pdb1Gdr/Pdb  1
1994 Rice PA, Steitz TA. Refinement of gamma delta resolvase reveals a strikingly flexible molecule. Structure (London, England : 1993). 2: 371-84. PMID 8081753 DOI: 10.2210/Pdb2Rsl/Pdb  1
1994 Wang J, Smerdon SJ, Jäger J, Kohlstaedt LA, Rice PA, Friedman JM, Steitz TA. Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer. Proceedings of the National Academy of Sciences of the United States of America. 91: 7242-6. PMID 7518928 DOI: 10.1073/Pnas.91.15.7242  1
1994 Smerdon SJ, Jäger J, Wang J, Kohlstaedt LA, Chirino AJ, Friedman JM, Rice PA, Steitz TA. Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1. Proceedings of the National Academy of Sciences of the United States of America. 91: 3911-5. PMID 7513427 DOI: 10.1073/Pnas.91.9.3911  1
1993 Hughes RE, Rice PA, Steitz TA, Grindley ND. Protein-protein interactions directing resolvase site-specific recombination: a structure-function analysis. The Embo Journal. 12: 1447-58. PMID 8385604 DOI: 10.1002/J.1460-2075.1993.Tb05788.X  1
1993 Steitz TA, Smerdon S, Jäger J, Wang J, Kohlstaedt LA, Friedman JM, Beese LS, Rice PA. Two DNA polymerases: HIV reverse transcriptase and the Klenow fragment of Escherichia coli DNA polymerase I. Cold Spring Harbor Symposia On Quantitative Biology. 58: 495-504. PMID 7525146 DOI: 10.1101/Sqb.1993.058.01.056  1
1993 Steitz TA, Kohlstaedt LA, Wang J, Friedman JM, Rice PA. Addendum: Crystal Structure at 3.5 overset{circ}{mathrm A} Resolution of HIV-1 Reverse Transcriptase Complexed with an Inhibitor Science. 259: 295. DOI: 10.1126/Science.259.5093.295  1
1993 Wang J, Smerdon SJ, Kohlstaedt LA, Jacger J, Rice PA, Friedman JM, Steitz TA. Structure of HIV reverse transcriptase Acta Crystallographica Section a Foundations of Crystallography. 49: c154-c154. DOI: 10.1107/S0108767378095598  1
1993 Kohlstaedt LA, Wang J, Rice PA, Friedman JM, Steitz TA. 12 The Structure of HIV-1 Reverse Transcriptase Cold Spring Harbor Monograph Archive. 23: 223-249. DOI: 10.1101/087969382.23.223  1
1993 steitz TA, Kohlstaedt LA, Wang J, Rice PA, Boisvert D, Friedman JM. Hiv reverse transcriptase: Structure and specificity for trna Protein Engineering, Design and Selection. 6: 108. DOI: 10.1093/protein/6.Supplement.108  1
1992 Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science (New York, N.Y.). 256: 1783-90. PMID 1377403 DOI: 10.1126/Science.1377403  1
1990 Hughes RE, Hatfull GF, Rice P, Steitz TA, Grindley ND. Cooperativity mutants of the gamma delta resolvase identify an essential interdimer interaction. Cell. 63: 1331-8. PMID 2175679 DOI: 10.1016/0092-8674(90)90428-H  1
1990 Sanderson MR, Freemont PS, Rice PA, Goldman A, Hatfull GF, Grindley ND, Steitz TA. The crystal structure of the catalytic domain of the site-specific recombination enzyme gamma delta resolvase at 2.7 A resolution. Cell. 63: 1323-9. PMID 2175678 DOI: 10.1016/0092-8674(90)90427-G  1
1990 Rice PA, Goldman A, Steitz TA. A helix-turn-strand structural motif common in alpha-beta proteins. Proteins. 8: 334-40. PMID 1708883 DOI: 10.1002/Prot.340080407  1
1989 Rice PA, Steitz TA. Ribosomal protein L7/L12 has a helix-turn-helix motif similar to that found in DNA-binding regulatory proteins. Nucleic Acids Research. 17: 3757-62. PMID 2660100 DOI: 10.1093/Nar/17.10.3757  1
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