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3R8F

Replication initiator DnaA bound to AMPPCP and single-stranded DNA

Summary for 3R8F
Entry DOI10.2210/pdb3r8f/pdb
DescriptorChromosomal replication initiator protein dnaA, 5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3', MAGNESIUM ION, ... (5 entities in total)
Functional Keywordsaaa+ atpase, replication initiator, dna binding, replication activator-dna complex, replication activator/dna
Biological sourceAquifex aeolicus
Cellular locationCytoplasm: O66659
Total number of polymer chains5
Total formula weight157279.51
Authors
Duderstadt, K.E.,Chuang, K.,Berger, J.M. (deposition date: 2011-03-23, release date: 2011-09-28, Last modification date: 2023-09-13)
Primary citationDuderstadt, K.E.,Chuang, K.,Berger, J.M.
DNA stretching by bacterial initiators promotes replication origin opening.
Nature, 478:209-213, 2011
Cited by
PubMed Abstract: Many replication initiators form higher-order oligomers that process host replication origins to promote replisome formation. In addition to dedicated duplex-DNA-binding domains, cellular initiators possess AAA+ (ATPases associated with various cellular activities) elements that drive functions ranging from protein assembly to origin recognition. In bacteria, the AAA+ domain of the initiator DnaA has been proposed to assist in single-stranded DNA formation during origin melting. Here we show crystallographically and in solution that the ATP-dependent assembly of Aquifex aeolicus DnaA into a spiral oligomer creates a continuous surface that allows successive AAA+ domains to bind and extend single-stranded DNA segments. The mechanism of binding is unexpectedly similar to that of RecA, a homologous recombination factor, but it differs in that DnaA promotes a nucleic acid conformation that prevents pairing of a complementary strand. These findings, combined with strand-displacement assays, indicate that DnaA opens replication origins by a direct ATP-dependent stretching mechanism. Comparative studies reveal notable commonalities between the approach used by DnaA to engage DNA substrates and other, nucleic-acid-dependent, AAA+ systems.
PubMed: 21964332
DOI: 10.1038/nature10455
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (3.366 Å)
Structure validation

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