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Int. J. Mol. Sci. 2015, 16(11), 27897-27911; doi:10.3390/ijms161126064

Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin

1
Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center, Washington, DC 20007, USA
2
Department of Biological Sciences, Florida Institute of Technology, 150 West University Blvd, Melbourne, FL 32901, USA
3
Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Christo Z. Christov
Received: 28 July 2015 / Revised: 21 October 2015 / Accepted: 16 November 2015 / Published: 24 November 2015
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
View Full-Text   |   Download PDF [1833 KB, uploaded 24 November 2015]   |  

Abstract

DnaA oligomerizes when bound to origins of chromosomal replication. Structural analysis of a truncated form of DnaA from Aquifex aeolicus has provided insight into crucial conformational differences within the AAA+ domain that are specific to the ATP- versus ADP- bound form of DnaA. In this study molecular docking of ATP and ADP onto Escherichia coli DnaA, modeled on the crystal structure of Aquifex aeolicus DnaA, reveals changes in the orientation of amino acid residues within or near the vicinity of the nucleotide-binding pocket. Upon limited proteolysis with trypsin or chymotrypsin ADP-DnaA, but not ATP-DnaA generated relatively stable proteolytic fragments of various sizes. Examined sites of limited protease susceptibility that differ between ATP-DnaA and ADP-DnaA largely reside in the amino terminal half of DnaA. The concentration of adenine nucleotide needed to induce conformational changes, as detected by these protease susceptibilities of DnaA, coincides with the conversion of an inactive bacterial origin recognition complex (bORC) to a replication efficient pre-replication complex (pre-RC) at the E. coli chromosomal origin of replication (oriC). View Full-Text
Keywords: DnaA protein; AAA+ domain; molecular docking; proteolysis; chromosomal origin; DNA replication DnaA protein; AAA+ domain; molecular docking; proteolysis; chromosomal origin; DNA replication
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Saxena, R.; Vasudevan, S.; Patil, D.; Ashoura, N.; Grimwade, J.E.; Crooke, E. Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin. Int. J. Mol. Sci. 2015, 16, 27897-27911.

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