Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin
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 mo...
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doaj-9e40f67566af48239b93697a2529142c2020-11-24T21:11:58ZengMDPI AGInternational Journal of Molecular Sciences1422-00672015-11-011611278972791110.3390/ijms161126064ijms161126064Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal OriginRahul Saxena0Sona Vasudevan1Digvijay Patil2Norah Ashoura3Julia E. Grimwade4Elliott Crooke5Department of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center, Washington, DC 20007, USADepartment of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center, Washington, DC 20007, USADepartment of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center, Washington, DC 20007, USADepartment of Biological Sciences, Florida Institute of Technology, 150 West University Blvd, Melbourne, FL 32901, USADepartment of Biological Sciences, Florida Institute of Technology, 150 West University Blvd, Melbourne, FL 32901, USADepartment of Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center, Washington, DC 20007, USADnaA 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).http://www.mdpi.com/1422-0067/16/11/26064DnaA proteinAAA+ domainmolecular dockingproteolysischromosomal originDNA replication |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Rahul Saxena Sona Vasudevan Digvijay Patil Norah Ashoura Julia E. Grimwade Elliott Crooke |
spellingShingle |
Rahul Saxena Sona Vasudevan Digvijay Patil Norah Ashoura Julia E. Grimwade Elliott Crooke Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin International Journal of Molecular Sciences DnaA protein AAA+ domain molecular docking proteolysis chromosomal origin DNA replication |
author_facet |
Rahul Saxena Sona Vasudevan Digvijay Patil Norah Ashoura Julia E. Grimwade Elliott Crooke |
author_sort |
Rahul Saxena |
title |
Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin |
title_short |
Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin |
title_full |
Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin |
title_fullStr |
Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin |
title_full_unstemmed |
Nucleotide-Induced Conformational Changes in Escherichia coli DnaA Protein Are Required for Bacterial ORC to Pre-RC Conversion at the Chromosomal Origin |
title_sort |
nucleotide-induced conformational changes in escherichia coli dnaa protein are required for bacterial orc to pre-rc conversion at the chromosomal origin |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2015-11-01 |
description |
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). |
topic |
DnaA protein AAA+ domain molecular docking proteolysis chromosomal origin DNA replication |
url |
http://www.mdpi.com/1422-0067/16/11/26064 |
work_keys_str_mv |
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