2D7G

Crystal structure of the aa complex of the N-terminal domain of PriA

Summary for 2D7G

• Entry DOI: 10.2210/pdb2d7g/pdb
• Related: 2D7H
• Descriptor: Primosomal protein N', DNA (5'-D(P*AP*A)-3') (2 entities in total)
• Functional Keywords: protein-dna complex, hydrolase
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 8
• Total formula weight: 49432.98

Authors

Sasaki, K.,Ose, T.,Maenaka, K.,Masai, H.,Kohda, D. (deposition date: 2005-11-21, release date: 2006-11-07, Last modification date: 2024-03-13)

Primary citation

Sasaki, K.,Ose, T.,Okamoto, N.,Maenaka, K.,Tanaka, T.,Masai, H.,Saito, M.,Shirai, T.,Kohda, D.
Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA.
EMBO J., 26:2584-2593, 2007

PubMed Abstract: In eubacteria, PriA helicase detects the stalled DNA replication forks. This critical role of PriA is ascribed to its ability to bind to the 3' end of a nascent leading DNA strand in the stalled replication forks. The crystal structures in complexes with oligonucleotides and the combination of fluorescence correlation spectroscopy and mutagenesis reveal that the N-terminal domain of PriA possesses a binding pocket for the 3'-terminal nucleotide residue of DNA. The interaction with the deoxyribose 3'-OH is essential for the 3'-terminal recognition. In contrast, the direct interaction with 3'-end nucleobase is unexpected, considering the same affinity for oligonucleotides carrying the four bases at the 3' end. Thus, the N-terminal domain of PriA recognizes the 3'-end base in a base-non-selective manner, in addition to the deoxyribose and 5'-side phosphodiester group, of the 3'-terminal nucleotide to acquire both sufficient affinity and non-selectivity to find all of the stalled replication forks generated during DNA duplication. This unique feature is prerequisite for the proper positioning of the helicase domain of PriA on the unreplicated double-stranded DNA.

PubMed: 17464287
DOI: 10.1038/sj.emboj.7601697

Experimental method

X-RAY DIFFRACTION (3.3 Å)