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Phoebe A. Rice

TitlePROFESSOR
InstitutionUniversity of Chicago
DepartmentBiochem/Mol Bio
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    Collapse Overview 
    Collapse overview
    How do mobile genetic elements jump? We use biochemistry, structural biology, and microbiology to get mechanistic answers. Projects include the SCCmec element of MRSA and the paradigmatic Mu transposase.


    Collapse Biography 
    Collapse education and training
    NIH / NIDDK, Bethesda, MDpost-doctoral1997Transposition Biochemistry
    Yale University, New Haven, CTPhD1992Molecular Biophysics & Biochemistry
    Brandeis University, Waltham, MABA1986Biochemistry
    Collapse awards and honors
    2015Distinguished Educator in the Basic Sciences, University of Chicago, Biological Sciences Division
    1987NSF fellowship
    1982 - 1986Gannett Newspaper Carrier Scholarship

    Collapse ORNG Applications 
    Collapse Websites

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Cao Y, Qiu T, Kathayat RS, Azizi SA, Thorne AK, Ahn D, Fukata Y, Fukata M, Rice PA, Dickinson BC. ABHD10 is an S-depalmitoylase affecting redox homeostasis through peroxiredoxin-5. Nat Chem Biol. 2019 Dec; 15(12):1232-1240. PMID: 31740833.
      View in: PubMed
    2. Rice PA. Structure of the P element transpososome reveals new twists on the DD(E/D) theme. Nat Struct Mol Biol. 2019 Nov; 26(11):989-990. PMID: 31659331.
      View in: PubMed
    3. Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins. 2019 Dec; 87(12):1037-1057. PMID: 31442339.
      View in: PubMed
    4. Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun. 2019 08 09; 10(1):3629. PMID: 31399592.
      View in: PubMed
    5. Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM. Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA. Biochemistry. 2019 Apr 16; 58(15):1963-1974. PMID: 30950607.
      View in: PubMed
    6. Connolly M, Arra A, Zvoda V, Steinbach PJ, Rice PA, Ansari A. Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements. J Phys Chem B. 2018 12 13; 122(49):11519-11534. PMID: 30336035.
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    7. Dyda F, Rice PA. A new twist on V(D)J recombination. Nat Struct Mol Biol. 2018 08; 25(8):648-649. PMID: 30061601.
      View in: PubMed
    8. Mir-Sanchis I, Pigli YZ, Rice PA. Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements. Structure. 2018 08 07; 26(8):1144-1150.e3. PMID: 30017563.
      View in: PubMed
    9. Trejo CS, Rock RS, Stark WM, Boocock MR, Rice PA. Snapshots of a molecular swivel in action. Nucleic Acids Res. 2018 06 01; 46(10):5286-5296. PMID: 29315406.
      View in: PubMed
    10. Rasila TS, Pulkkinen E, Kiljunen S, Haapa-Paananen S, Pajunen MI, Salminen A, Paulin L, Vihinen M, Rice PA, Savilahti H. Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering. Nucleic Acids Res. 2018 05 18; 46(9):4649-4661. PMID: 29294068.
      View in: PubMed
    11. Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein. Nucleic Acids Res. 2018 02 28; 46(4):1741-1755. PMID: 29267885.
      View in: PubMed
    12. Toussaint A, Rice PA. Transposable phages, DNA reorganization and transfer. Curr Opin Microbiol. 2017 Aug; 38:88-94. PMID: 28551392.
      View in: PubMed
    13. Fuller JR, Rice PA. Target DNA bending by the Mu transpososome promotes careful transposition and prevents its reversal. Elife. 2017 02 13; 6. PMID: 28177285.
      View in: PubMed
    14. 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. Nat Struct Mol Biol. 2016 Oct; 23(10):891-898. PMID: 27571176.
      View in: PubMed
    15. Arkhipova IR, Rice PA. Mobile genetic elements: in silico, in vitro, in vivo. Mol Ecol. 2016 Mar; 25(5):1027-31. PMID: 26822117.
      View in: PubMed
    16. Suslov NB, DasGupta S, Huang H, Fuller JR, Lilley DM, Rice PA, Piccirilli JA. Crystal structure of the Varkud satellite ribozyme. Nat Chem Biol. 2015 Nov; 11(11):840-6. PMID: 26414446.
      View in: PubMed
    17. Rice PA. Serine Resolvases. Microbiol Spectr. 2015 Apr; 3(2):MDNA3-0045-2014. PMID: 26104713.
      View in: PubMed
    18. Ling L, Montaño SP, Sauer RT, Rice PA, Baker TA. Deciphering the Roles of Multicomponent Recognition Signals by the AAA+ Unfoldase ClpX. J Mol Biol. 2015 Sep 11; 427(18):2966-82. PMID: 25797169.
      View in: PubMed
    19. 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. Nat Chem Biol. 2014 Aug; 10(8):686-91. PMID: 24952597.
      View in: PubMed
    20. Boocock MR, Rice PA. A proposed mechanism for IS607-family serine transposases. Mob DNA. 2013 Nov 06; 4(1):24. PMID: 24195768.
      View in: PubMed
    21. 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. J Chem Phys. 2013 Sep 28; 139(12):121927. PMID: 24089739.
      View in: PubMed
    22. Keenholtz RA, Mouw KW, Boocock MR, Li NS, Piccirilli JA, Rice PA. Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage. J Biol Chem. 2013 Oct 04; 288(40):29206-14. PMID: 23970547.
      View in: PubMed
    23. 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. Mol Microbiol. 2013 Jun; 88(6):1218-29. PMID: 23651464.
      View in: PubMed
    24. Montaño SP, Pigli YZ, Rice PA. The µ transpososome structure sheds light on DDE recombinase evolution. Nature. 2012 Nov 15; 491(7424):413-7. PMID: 23135398.
      View in: PubMed
    25. Vivas P, Velmurugu Y, Kuznetsov SV, Rice PA, Ansari A. Mapping the transition state for DNA bending by IHF. J Mol Biol. 2012 May 18; 418(5):300-15. PMID: 22370561.
      View in: PubMed
    26. 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. Biophys J. 2011 Aug 17; 101(4):899-909. PMID: 21843481.
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    27. Flott S, Kwon Y, Pigli YZ, Rice PA, Sung P, Jackson SP. Regulation of Rad51 function by phosphorylation. EMBO Rep. 2011 Jul 08; 12(8):833-9. PMID: 21738226.
      View in: PubMed
    28. Keenholtz RA, Rowland SJ, Boocock MR, Stark WM, Rice PA. Structural basis for catalytic activation of a serine recombinase. Structure. 2011 Jun 08; 19(6):799-809. PMID: 21645851.
      View in: PubMed
    29. Montaño SP, Rice PA. Moving DNA around: DNA transposition and retroviral integration. Curr Opin Struct Biol. 2011 Jun; 21(3):370-8. PMID: 21439812.
      View in: PubMed
    30. 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. J Mol Biol. 2010 Nov 19; 404(1):16-33. PMID: 20868695.
      View in: PubMed
    31. Chaconas G, Craig N, Curcio MJ, Deininger P, Feschotte C, Levin H, Rice PA, Voytas DF. Meeting report for mobile DNA 2010. Mob DNA. 2010 Aug 24; 1(1):20. PMID: 20735816.
      View in: PubMed
    32. Zhang AP, Pigli YZ, Rice PA. Structure of the LexA-DNA complex and implications for SOS box measurement. Nature. 2010 Aug 12; 466(7308):883-6. PMID: 20703307.
      View in: PubMed
    33. Rice PA, Mouw KW, Montaño SP, Boocock MR, Rowland SJ, Stark WM. Orchestrating serine resolvases. Biochem Soc Trans. 2010 Apr; 38(2):384-7. PMID: 20298188.
      View in: PubMed
    34. 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. J Biol Chem. 2009 Aug 28; 284(35):23517-24. PMID: 19586910.
      View in: PubMed
    35. 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. Mol Microbiol. 2009 Oct; 74(2):282-98. PMID: 19508283.
      View in: PubMed
    36. Grigorescu AA, Vissers JH, Ristic D, Pigli YZ, Lynch TW, Wyman C, Rice PA. Inter-subunit interactions that coordinate Rad51's activities. Nucleic Acids Res. 2009 Feb; 37(2):557-67. PMID: 19066203.
      View in: PubMed
    37. Peng X, Pigli YZ, Rice PA, Greenberg MM. Protein binding has a large effect on radical mediated DNA damage. J Am Chem Soc. 2008 Oct 01; 130(39):12890-1. PMID: 18778053.
      View in: PubMed
    38. Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA. Architecture of a serine recombinase-DNA regulatory complex. Mol Cell. 2008 Apr 25; 30(2):145-55. PMID: 18439894.
      View in: PubMed
    39. 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. 2008 Apr 24; 452(7190):961-5. PMID: 18432238.
      View in: PubMed
    40. Whiteson KL, Rice PA. Binding and catalytic contributions to site recognition by flp recombinase. J Biol Chem. 2008 Apr 25; 283(17):11414-23. PMID: 18276592.
      View in: PubMed
    41. 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. Proc Natl Acad Sci U S A. 2007 Sep 11; 104(37):14622-7. PMID: 17785414.
      View in: PubMed
    42. 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. Chem Biol. 2007 Feb; 14(2):121-9. PMID: 17317566.
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    43. Mouw KW, Rice PA. Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb. Mol Microbiol. 2007 Mar; 63(5):1319-30. PMID: 17244195.
      View in: PubMed
    44. Khrapunov S, Brenowitz M, Rice PA, Catalano CE. Binding then bending: a mechanism for wrapping DNA. Proc Natl Acad Sci U S A. 2006 Dec 19; 103(51):19217-8. PMID: 17159146.
      View in: PubMed
    45. Swinger KK, Rice PA. Structure-based analysis of HU-DNA binding. J Mol Biol. 2007 Jan 26; 365(4):1005-16. PMID: 17097674.
      View in: PubMed
    46. Lu CP, Sandoval H, Brandt VL, Rice PA, Roth DB. Amino acid residues in Rag1 crucial for DNA hairpin formation. Nat Struct Mol Biol. 2006 Nov; 13(11):1010-5. PMID: 17028591.
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    47. 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. Nat Chem Biol. 2006 Nov; 2(11):591-5. PMID: 16980961.
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    48. Grindley ND, Whiteson KL, Rice PA. Mechanisms of site-specific recombination. Annu Rev Biochem. 2006; 75:567-605. PMID: 16756503.
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    49. Rice PA. Resolving integral questions in site-specific recombination. Nat Struct Mol Biol. 2005 Aug; 12(8):641-3. PMID: 16077726.
      View in: PubMed
    50. Duguid EM, Rice PA, He C. The structure of the human AGT protein bound to DNA and its implications for damage detection. J Mol Biol. 2005 Jul 22; 350(4):657-66. PMID: 15964013.
      View in: PubMed
    51. Rice PA. Visualizing Mu transposition: assembling the puzzle pieces. Genes Dev. 2005 Apr 01; 19(7):773-5. PMID: 15805467.
      View in: PubMed
    52. Conway AB, Lynch TW, Zhang Y, Fortin GS, Fung CW, Symington LS, Rice PA. Crystal structure of a Rad51 filament. Nat Struct Mol Biol. 2004 Aug; 11(8):791-6. PMID: 15235592.
      View in: PubMed
    53. Swinger KK, Rice PA. IHF and HU: flexible architects of bent DNA. Curr Opin Struct Biol. 2004 Feb; 14(1):28-35. PMID: 15102446.
      View in: PubMed
    54. Swinger KK, Lemberg KM, Zhang Y, Rice PA. Flexible DNA bending in HU-DNA cocrystal structures. EMBO J. 2003 Jul 15; 22(14):3749-60. PMID: 12853489.
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    55. Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA. Integration host factor: putting a twist on protein-DNA recognition. J Mol Biol. 2003 Jul 11; 330(3):493-502. PMID: 12842466.
      View in: PubMed
    56. Chen Y, Rice PA. The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis. J Biol Chem. 2003 Jul 04; 278(27):24800-7. PMID: 12716882.
      View in: PubMed
    57. Conway AB, Chen Y, Rice PA. Structural plasticity of the Flp-Holliday junction complex. J Mol Biol. 2003 Feb 14; 326(2):425-34. PMID: 12559911.
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    58. Chen Y, Rice PA. New insight into site-specific recombination from Flp recombinase-DNA structures. Annu Rev Biophys Biomol Struct. 2003; 32:135-59. PMID: 12598365.
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    59. 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 Crystallogr D Biol Crystallogr. 2001 Dec; 57(Pt 12):1881-4. PMID: 11717504.
      View in: PubMed
    60. Rice PA, Baker TA. Comparative architecture of transposase and integrase complexes. Nat Struct Biol. 2001 May; 8(5):302-7. PMID: 11774877.
      View in: PubMed
    61. 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. Mol Cell. 2000 Oct; 6(4):885-97. PMID: 11090626.
      View in: PubMed
    62. Rice PA. Holding damaged DNA together. Nat Struct Biol. 1999 Sep; 6(9):805-6. PMID: 10467087.
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    63. Ram S, Mackinnon FG, Gulati S, McQuillen DP, Vogel U, Frosch M, Elkins C, Guttormsen HK, Wetzler LM, Oppermann M, Pangburn MK, Rice PA. The contrasting mechanisms of serum resistance of Neisseria gonorrhoeae and group B Neisseria meningitidis. Mol Immunol. 1999 Sep-Oct; 36(13-14):915-28. PMID: 10698346.
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    64. Mühlecker W, Gulati S, McQuillen DP, Ram S, Rice PA, Reinhold VN. An essential saccharide binding domain for the mAb 2C7 established for Neisseria gonorrhoeae LOS by ES-MS and MSn. Glycobiology. 1999 Feb; 9(2):157-71. PMID: 9949193.
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    65. McQuillen DP, Gulati S, Ram S, Turner AK, Jani DB, Heeren TC, Rice PA. Complement processing and immunoglobulin binding to Neisseria gonorrhoeae determined in vitro simulates in vivo effects. J Infect Dis. 1999 Jan; 179(1):124-35. PMID: 9841831.
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    66. Rice PA. Making DNA do a U-turn: IHF and related proteins. Curr Opin Struct Biol. 1997 Feb; 7(1):86-93. PMID: 9032059.
      View in: PubMed
    67. Rice PA, Yang S, Mizuuchi K, Nash HA. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell. 1996 Dec 27; 87(7):1295-306. PMID: 8980235.
      View in: PubMed
    68. Rice P, Craigie R, Davies DR. Retroviral integrases and their cousins. Curr Opin Struct Biol. 1996 Feb; 6(1):76-83. PMID: 8696976.
      View in: PubMed
    69. Savilahti H, Rice PA, Mizuuchi K. The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J. 1995 Oct 02; 14(19):4893-903. PMID: 7588618.
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    70. Rice P, Mizuuchi K. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell. 1995 Jul 28; 82(2):209-20. PMID: 7628012.
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    71. 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. Proc Natl Acad Sci U S A. 1994 Jul 19; 91(15):7242-6. PMID: 7518928.
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    72. Rice PA, Steitz TA. Refinement of gamma delta resolvase reveals a strikingly flexible molecule. Structure. 1994 May 15; 2(5):371-84. PMID: 8081753.
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    73. 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. Proc Natl Acad Sci U S A. 1994 Apr 26; 91(9):3911-5. PMID: 7513427.
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    74. Rice PA, Steitz TA. Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits. EMBO J. 1994 Apr 01; 13(7):1514-24. PMID: 8156989.
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    75. Hughes RE, Rice PA, Steitz TA, Grindley ND. Protein-protein interactions directing resolvase site-specific recombination: a structure-function analysis. EMBO J. 1993 Apr; 12(4):1447-58. PMID: 8385604.
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    76. 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 Harb Symp Quant Biol. 1993; 58:495-504. PMID: 7525146.
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    77. 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. 1992 Jun 26; 256(5065):1783-90. PMID: 1377403.
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    78. Hughes RE, Hatfull GF, Rice P, Steitz TA, Grindley ND. Cooperativity mutants of the gamma delta resolvase identify an essential interdimer interaction. Cell. 1990 Dec 21; 63(6):1331-8. PMID: 2175679.
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    79. 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. 1990 Dec 21; 63(6):1323-9. PMID: 2175678.
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    80. Rice PA, Goldman A, Steitz TA. A helix-turn-strand structural motif common in alpha-beta proteins. Proteins. 1990; 8(4):334-40. PMID: 1708883.
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    81. 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 Res. 1989 May 25; 17(10):3757-62. PMID: 2660100.
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