Phoebe A Rice

We study mechanisms of DNA recombination and protein-DNA recognition, combining the tools of biochemistry and x-ray crystallography. Projects include:

Rad51 and its prokaryotic counterpart RecA are central players in repairing dsDNA breaks and rescuing stalled replication forks. They bind a single strand of DNA, then play molecular matchmaker to align it with a homologous sequence in duplex DNA. We determined the first structure of a filament of yeast Rad51, and are examining the details of the protein-protein interactions that activate its ATPase.

Flp is a tyrosine-based site-specific DNA recombinase. Such enzymes catalyze DNA inversions, deletions, and insertions, and are useful in genetic engineering. We determined the structure of a Flp tetramer bound to a DNA Holliday junction, and are now exploiting the trans assembly of Flp's active site to investigate its catalytic mechanism using synthetic tyrosine analogs.

Sin: not what you think. This is another site-specific recombinase, utterly unrelated to Flp, that comes from Staph. Aureus and helps stably maintain resistance plasmids. Sin has a remarkable sense of direction: it recombines two sites only if they lie on the same plasmid, and only if they are properly oriented. It does so by becoming activated only if part of a large, topologically complex complex. We have recently determined the structure of a Sin tetramer bridging the two regulatory Sin binding sites in the complex, and can now build a model for the entire complex.

IHF, HU and Hbb are major components of the bacterial nucleoid and serve as all-purpose DNA benders. Able to bend DNA by over 180, they are paradigms for studying DNA bending and indirect recognition. IHF and Hbb recognize specific DNA sequences through the sequence-dependent structural features of the DNA, whereas HU binds with little regard to sequence but strongly prefers certain distorted DNA structures.

We study mechanisms of DNA recombination and protein-DNA recognition, combining the tools of biochemistry and x-ray crystallography. Projects include:

Rad51 and its prokaryotic counterpart RecA are central players in repairing dsDNA breaks and rescuing stalled replication forks. They bind a single strand of DNA, then play molecular matchmaker to align it with a homologous sequence in duplex DNA. We determined the first structure of a filament of yeast Rad51, and are examining the details of the protein-protein interactions that activate its ATPase.

Flp is a tyrosine-based site-specific DNA recombinase. Such enzymes catalyze DNA inversions, deletions, and insertions, and are useful in genetic engineering. We determined the structure of a Flp tetramer bound to a DNA Holliday junction, and are now exploiting the trans assembly of Flp's active site to investigate its catalytic mechanism using synthetic tyrosine analogs.

Sin: not what you think. This is another site-specific recombinase, utterly unrelated to Flp, that comes from Staph. Aureus and helps stably maintain resistance plasmids. Sin has a remarkable sense of direction: it recombines two sites only if they lie on the same plasmid, and only if they are properly oriented. It does so by becoming activated only...

Kent W. Mouw, Sally J Rowland, Mark M. Gajjar, Martin R Boocock, Marshall Stark and Phoebe A. Rice. Architecture of a serine recombinase - DNA regulatory complex. Molecular Cell, Apr 25;30(2):145-55.(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. Apr 24;452(7190):961-5. (2008)  

Protein-Nucleic Aicd Interactions: Structural Biology. P.A. Rice and Carl C. Correll, editors. RSC Publishing, 2008 http://www.rsc.org/shop/books/2008/9780854042722.asp  

Whiteson, KL and Rice, PA. Binding and Catalytic Contributions to Site Recognition by Flp Recombinase. JBC, Apr 25;283(17):11414-23, 2008.  

Mouw KW and Rice, PA. Shaping the Borrelia burgdorferi genome: Crystal structure and binding properties of the DNA-bending protein Hbb. Molecular Microbiology 63, 1319-1339 (2007) 

Whiteson, K.L., Chen Y., Chopra, N., Raymond, A.C. and Rice, P.A. Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305. Chemistry & Biology 14, 121-129 (2007). 

Swinger, K.K. and Rice, P.A. Structure-based Analysis of HU-DNA binding. J. Mol. Biol. 365: 1005-1016 (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. Proc Natl Acad Sci U S A. 104:14622-14627 (2007) 

Lu CP, Sandoval H, Brandt VL, Rice PA, Roth DB. Amino acid residues in Rag1 crucial for DNA hairpin formation. Nat Struct Mol Biol. 13, 1010-5. (2006) 

Grindley, N.D., Whiteson, K.L., and Rice, P.A. Mechanisms of Site-Specific Recombination. Annu. Rev. Biochem. 75:567-605 (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. Nat Chem Biol. 2:591-595 (2006).  

Duguid, E.M., Rice, P.A., and He, C. The structure of the human AGT protein bound to DNA and its implications for damage detection. J. Mol. Biol. 350 pp.657-666 (2005). 

Conway, A.B., Lynch, T.W., Zhang, Y., Fortin, G.S., Fung, C.W., Symington, L.S. and Rice, P.A. Crystal structure of a Rad51 filament. Nature Struct & Mol. Biol. 11, p791-796 (2004). 

Swinger, K.K., Lemberg, K.M., Zhang, Y. and Rice, P.A. Flexible DNA bending in HU-DNA cocrystal structures. EMBO J. 22 (July 15 2003).  

Chen, Y., Narendra, U., Iype, L.E., Cox, M.M. and Rice, P.A. Crystal Structure of a Flp Recombinase-Holliday Junction Complex: Assembly of an Active Oligomer by Helix Swapping. Molecular Cell 6, 885-897 (2000).  

Kent W. Mouw, Sally J Rowland, Mark M. Gajjar, Martin R Boocock, Marshall Stark and Phoebe A. Rice. Architecture of a serine recombinase - DNA regulatory complex. Molecular Cell, Apr 25;30(2):145-55.(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. Apr 24;452(7190):961-5. (2008)  

Protein-Nucleic Aicd Interactions: Structural Biology. P.A. Rice and Carl C. Correll, editors. RSC Publishing, 2008 http://www.rsc.org/shop/books/2008/9780854042722.asp  

Whiteson, KL and Rice, PA. Binding and Catalytic Contributions to Site Recognition by Flp Recombinase. JBC, Apr 25;283(17):11414-23, 2008.  

Mouw KW and Rice, PA. Shaping the Borrelia burgdorferi genome: Crystal structure and binding properties of the DNA-bending protein Hbb. Molecular Microbiology 63, 1319-1339 (2007)