The overall goal is to provide a structural basis for understanding the mechanisms of initiation and elongation by DNA and RNA polymerases, their transitions from initiation to elongation phases, the regulation of polymerases by factors and the mechanisms by which these polymerases assure that the correct nucleotide is inserted. This objective will be achieved by determining the crystal structures of polymerases complexed with functionally associated proteins and bound to appropriate DNA or RNA substrates, as well as by appropriate biochemical experiments.
We aim to establish the structures of component assemblies of the replisome. These include a replication fork complex with DNA polymerase III, tau and a forked-DNA substrate, as well as the structure of the primasome that includes Thermus aquaticus DNAB helicase complexed with the DNAG primase bound to their DNA substrate. Additionally, the structure of the DNAB helicase bound to its DNA and nucleotide substrates as well as that of the clamp loading protein bound to its DNA substrate, sliding clamp and single-stranded DNA binding protein will be established. The structural basis of the initiation of DNA synthesis by the protein primed

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM057510-12
Application #
7647446
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
1998-07-01
Project End
2010-06-30
Budget Start
2009-07-01
Budget End
2010-06-30
Support Year
12
Fiscal Year
2009
Total Cost
$394,265
Indirect Cost
Name
Yale University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
043207562
City
New Haven
State
CT
Country
United States
Zip Code
06520
Zuo, Yuhong; Steitz, Thomas A (2015) Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Mol Cell 58:534-40
Liu, Bin; Zuo, Yuhong; Steitz, Thomas A (2015) Structural basis for transcription reactivation by RapA. Proc Natl Acad Sci U S A 112:2006-10
Ritacco, Christopher J; Steitz, Thomas A; Wang, Jimin (2014) Exploiting large non-isomorphous differences for phase determination of a G-segment invertase-DNA complex. Acta Crystallogr D Biol Crystallogr 70:685-93
Liu, Bin; Eliason, William K; Steitz, Thomas A (2013) Structure of a helicase-helicase loader complex reveals insights into the mechanism of bacterial primosome assembly. Nat Commun 4:2495
Zuo, Yuhong; Wang, Yeming; Steitz, Thomas A (2013) The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex. Mol Cell 50:430-6
Liu, Bin; Lin, Jinzhong; Steitz, Thomas A (2013) Structure of the PolIII?-?c-DNA complex suggests an atomic model of the replisome. Structure 21:658-64
Ritacco, Christopher J; Kamtekar, Satwik; Wang, Jimin et al. (2013) Crystal structure of an intermediate of rotating dimers within the synaptic tetramer of the G-segment invertase. Nucleic Acids Res 41:2673-82
Itsathitphaisarn, Ornchuma; Wing, Richard A; Eliason, William K et al. (2012) The hexameric helicase DnaB adopts a nonplanar conformation during translocation. Cell 151:267-77
Wang, Mina; Xia, Shuangluo; Blaha, Gregor et al. (2011) Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex. Biochemistry 50:581-90
Pan, Baocheng; Xiong, Yong; Steitz, Thomas A (2010) How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA. Science 330:937-40

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