PDBsum entry 1xrx

Replication inhibitor

PDB id: 1xrx

Contents

Protein chains

35 a.a. *

Metals

_CA

Waters ×175

* Residue conservation analysis

PDB id:

1xrx

Name:

Replication inhibitor

Title:

Crystal structure of a DNA-binding protein

Structure:

Seqa protein. Chain: a, b, c, d. Fragment: n-terminal domain. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: seqa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.15Å R-factor: 0.222 R-free: 0.237

Authors:

A.Guarne,T.Brendler,Q.Zhao,R.Ghirlando,S.Austin,W.Yang

Key ref:

A.Guarné et al. (2005). Crystal structure of a SeqA-N filament: implications for DNA replication and chromosome organization. EMBO J, 24, 1502-1511. PubMed id: 15933720 DOI: 10.1038/sj.emboj.7600634

Date:

16-Oct-04 Release date: 10-May-05

Protein chains

P0AFY8  (SEQA_ECOLI) -  Negative modulator of initiation of replication from Escherichia coli (strain K12)

Seq: 181 a.a.

Struc: 35 a.a.

DOI no: 10.1038/sj.emboj.7600634

EMBO J 24:1502-1511 (2005)

PubMed id: 15933720

Crystal structure of a SeqA-N filament: implications for DNA replication and chromosome organization.

A.Guarné, T.Brendler, Q.Zhao, R.Ghirlando, S.Austin, W.Yang.

ABSTRACT

Escherichia coli SeqA binds clusters of transiently hemimethylated GATC sequences and sequesters the origin of replication, oriC, from methylation and premature reinitiation. Besides oriC, SeqA binds and organizes newly synthesized DNA at replication forks. Binding to multiple GATC sites is crucial for the formation of stable SeqA-DNA complexes. Here we report the crystal structure of the oligomerization domain of SeqA (SeqA-N). The structural unit of SeqA-N is a dimer, which oligomerizes to form a filament. Mutations that disrupt filament formation lead to asynchronous DNA replication, but the resulting SeqA dimer can still bind two GATC sites separated from 5 to 34 base pairs. Truncation of the linker between the oligomerization and DNA-binding domains restricts SeqA to bind two GATC sites separated by one or two full turns. We propose a model of a SeqA filament interacting with multiple GATC sites that accounts for both origin sequestration and chromosome organization.

Selected figure(s)

Figure 1.
Figure 1 Oligomerization of the SeqA -N dimer. (A) Ribbon diagram of a single SeqA -N subunit. (B) A SeqA -N dimer. The two subunits are shown as yellow and green ribbon diagrams. (C) The asymmetric unit contains two SeqA -N dimers related by a noncrystallographic dyad axis and a 4[3] screw axis. The two SeqA -N dimers colored yellow -green and blue -red, respectively, are shown in a ribbons diagram (left) and molecular surface representation (right). (D) Two views of the SeqA -N filament. The black bar indicates a complete helical turn consisting of four dimers. The 4[3] axis and the noncrystallographic (gray arrows) and crystallographic (gray ovals) dyad axes are indicated. (E) Crystal packing of the SeqA filaments shown as a ribbon diagram. Filaments pack according to the crystallographic 3[1] axis. The central filament is shown with the SeqA monomers colored yellow and green. The top and bottom filaments are shown in light and dark gray, respectively.

Figure 5.
Figure 5 A model of the interactions between a SeqA filament and DNA. (A) A SeqA -N dimer and a pair of crystallographic SeqA -C -DNA complexes are placed to share a common dyad axis. The protein is shown as ribbon diagrams in dark (SeqA -N) and light (SeqA -C) blue and the DNA depicted as stick models. (B) The full-length SeqA dimer -DNA model is allowed to multimerize according to the 4[3] screw axis of the SeqA -N filament. The four-fold screw axis is perpendicular to the plane. Each SeqA -N dimer and the SeqA -C pair bound to it are shown in dark and light shades of a distinct color. Space between the N- and C-terminal domains accounts for the flexible linker and avoids contacts or clashes between neighboring SeqA -C molecules related by the 4[3] screw axis. An orthogonal view placing the SeqA -DNA superhelix in plane is shown on the right panel. No artificial coordinates are introduced, and DNAs are left to be discontinuous between adjacent SeqA dimers. Scale bars represent 100 Å.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2005, 24, 1502-1511) copyright 2005.

Figures were selected by the author.