The Faculty


Structural biochemistry of DNA recombination


B.A., Biochemistry Brandeis University, 1986

Ph.D., Molecular Biophysics and Biochemistry Yale University, 1992

Post-doctoral fellow at LMB/NIDDK/NIH 1993-1997

Research Summary

We combine biochemistry and x-ray crystallography to study protein-DNA interactions and DNA recombination.

Site-specific DNA recombinases: These cut and paste DNA at defined sequences, and are useful genetic tools. They exchange DNA partners via a remarkable molecular swivel. Two favorites are:
(1) Sin, which aids stable maintenance of multi-resistance plasmids of S. aureus. Sin is regulated by the global topology of its plasmid substrate. In collaboration with the Stark group in Glasgow, we are using kinetics, crystallography, and molecular modeling to understand this enzyme at the molecular level.
(2) CcrA/B/C, which mobilize the methicillin-resistance encoding element that turns garden-variety S. aureus into MRSA. Their catalytic domain is related to Sin’s, but their regulation is very different and rather mysterious. This is a local collaboration with Drs. Daum and Boyle- Vavra, who study the epidemiology of MRSA.

“classical” DNA transposases: members of this family are closely related to retroviral integrases. They catalyze the mobility of numerous DNA transposons, contributing to horizontal gene transfer and antibiotic resistance in bacteria.
Rad51 and its prokaryotic counterpart RecA , repair dsDNA breaks and rescue 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.

LexA, the master regulator of the bacterial DNA damage response and a potential antibiotic target. LexA is a transcriptional repressor that cleaves itself when it contacts active RecA filaments. We recently determined the structure of LexA bound to an SOS box, and are working to understand its interactions with RecA, and the surprising variety of SOS systems found in diverse bacteria.

Selected Publications

Chen, Y., Narendra, U., Ipye, 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).  (featured on the cover)

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

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) PMCID:PMC2587245

Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark M and Rice, PA. Architecture of a serine recombinase - DNA regulatory complex. Mol Cell. Apr 25;30(2):145-55. (2008) PMCID: PMC2428073

featured on the journal cover and highlighted in Structure: Assembly of a tightly interwound DNA recombination complex poised for deletion. Johnson RC, Heiss JK. Structure. 2008 May;16(5):653-5.

Rowland, S-J, Boocock, MR, McPherson, AL, Mouw, KW, Rice, PA and Stark, WM. Regulatory mutations in Sin recombinase support a srtructure-based model of the synaptosome. Mol Microbiol. 74, 282-98. (2009). PMCID:PMC2764113

Swinger KK, Lemberg, KM, Zhang, Y and Rice, PA.  Flexible DNA bending in HU-DNA cocrystal structures.  EMBO J 22, 3749-3760 (2003).

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).  

Whiteson, KL and Rice, PA. Binding and Catalytic Contributions to Site Recognition by Flp Recombinase.  J Biol Chem. Apr 25;283(17):11414-23 (2008). PMCID: PMC2431069

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. 37(2):557-67. (2009). PMCID: PMC2921665

Mouw KW, Steiner AM, Ghirlando R, Li N-S, Rowland S-J, Boocock MR, Stark WM, Piccirilli JA and Rice PA. Sin Resolvase Catalytic Activity and Oligomerization State are Tightly Coupled. JMB 404(1):16-33. (2010). PMCID: PMC2976518

Zhang APP, Pigli YZ, and Rice PA. Structure of the LexA–DNA complex structure and implications for SOS box measurement Nature, 466(7308):883-6 (2010). PMCID: PMC2921665

Keenholtz RK, Rowland S-J, Boocock MR, Stark WM, and Rice PA. Structural basis for catalytic activation of a serine recombinase.  Structure, 19(6): 799-809 (2011).  PMCID: PMC3238390

Highlighted in an accompanying Preview: Recombining DNA by protein swivels. Johnson RC, McLean MM.  Structure. 19(6):751-3 (2011).

Haddadian EJ, Gong H, Jha AK, Yang XJ, DeBartolo J, Hinshaw JR, Rice PA,  Sosnick TR and Freed KF. Automated real-space refinement of protein structures using a realistic backbone move set.  Biophys J. 101(4):899-909. (2011) PMCID:PMC3175057

Vivas P, Velmurugu Y, Kuznetxov SV, Rice PA and Ansari A. Mapping the transition state for DNA bending by IHF.  JMB, 418(5):300-15 (2012).  PMCID in process

Montaño, SP, Pigli, YZ, and Rice, PA.  Structure of the Mu transpososome illuminates evolution of DDE recombinases.  Nature, Nov 15;491(7424):413-7. (2012) PMCID:PMC3536463