title: Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin.
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).
authors.affiliation: Department of Biochemistry and Molecular &amp; Cellular Biology Georgetown University Medical Center, Washington, DC 20007, USA. rs426@georgetown.edu.
authors.forename: Rahul
authors.initials: R
authors.lastname: Saxena
authors.affiliation: Department of Biochemistry and Molecular &amp; Cellular Biology Georgetown University Medical Center, Washington, DC 20007, USA. sv67@georgetown.edu.
authors.forename: Sona
authors.initials: S
authors.lastname: Vasudevan
authors.affiliation: Department of Biochemistry and Molecular &amp; Cellular Biology Georgetown University Medical Center, Washington, DC 20007, USA. dap89@georgetown.edu.
authors.forename: Digvijay
authors.initials: D
authors.lastname: Patil
authors.affiliation: Department of Biological Sciences, Florida Institute of Technology, 150 West University Blvd, Melbourne, FL 32901, USA. nashoura2010@utexas.edu.
authors.forename: Norah
authors.initials: N
authors.lastname: Ashoura
authors.affiliation: Department of Biological Sciences, Florida Institute of Technology, 150 West University Blvd, Melbourne, FL 32901, USA. grimwade@fit.edu.
authors.forename: Julia E
authors.initials: JE
authors.lastname: Grimwade
authors.affiliation: Department of Biochemistry and Molecular &amp; Cellular Biology Georgetown University Medical Center, Washington, DC 20007, USA. crooke@georgetown.edu.|Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA. crooke@georgetown.edu.
authors.forename: Elliott
authors.initials: E
authors.lastname: Crooke
mesh_terms: D000244:Adenosine Diphosphate / Q000737:chemistry / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002236:Carbohydrate Conformation; D002876:Chromosomes, Bacterial; D004261:DNA Replication; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D008958:Models, Molecular; D009698:Nucleoproteins / Q000378:metabolism; D009711:Nucleotides / Q000737:chemistry* / Q000378:metabolism; D051738:Origin Recognition Complex / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D059748:Proteolysis; D018741:Replication Origin
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C066312:DnaA protein, Bacteria; D009698:Nucleoproteins; D009711:Nucleotides; D051738:Origin Recognition Complex; D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate
keywords: AAA+ domain; DNA replication; DnaA protein; chromosomal origin; molecular docking; proteolysis