SNAP output for PDB entry 1lrr [SNAP web server]

PDB-id

1lrr; SNAP-derived features in text and JSON formats; DNAproDB

Class

replication inhibitor-DNA

Method

X-ray (2.65 Å)

Summary

Crystal structure of e. coli seqa complexed with hemimethylated DNA

Reference

Guarne A, Zhao Q, Guirlando R, Yang W (2002): "Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex." NAT.STRUCT.BIOL., 9, 839-843.

Abstract

The SeqA protein binds clusters of fully methylated or hemimethylated GATC sequences at oriC and negatively modulates the initiation of DNA replication. We find that SeqA can be proteolytically cleaved into an N-terminal multimerization and a C-terminal DNA-binding domain and have determined the crystal structure of the C-terminal domain in complex with a hemimethylated GATC site. SeqA makes direct hydrogen bonds and van der Waals contacts with the hemimethylated A-T base pair in addition to interactions with the surrounding bases and DNA backbone. The tetrameric protein-DNA complex found in the crystal suggests that SeqA binds multiple GATC sites on separate DNA duplexes, altering the overall DNA topology and sequestering oriC from replication initiation.