PDBsum entry 1rep

Replication/DNA

PDB id: 1rep

Contents

Protein chain

214 a.a. *

DNA/RNA

Metals

_MG

Waters ×20

* Residue conservation analysis

PDB id:

1rep

Name:

Replication/DNA

Title:

Crystal structure of replication initiator protein repe54 of mini-f plasmid complexed with an iteron DNA

Structure:

DNA (5'- d( Cp Cp Tp Gp Tp Gp Ap Cp Ap Ap Ap Tp Tp Gp Cp Cp Cp Tp Cp Ap Gp T)- 3'). Chain: a. Synonym: iteron. Engineered: yes. DNA (5'- d( Cp Tp Gp Ap Gp Gp Gp Cp Ap Ap Tp Tp Tp Gp Tp Cp Ap Cp Ap Gp Gp T)- 3').

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: his-tagged protein

Biol. unit:

Hexamer (from PQS)

Resolution:

2.60Å R-factor: 0.213 R-free: 0.274

Authors:

H.Komori,F.Matsunaga,Y.Higuchi,M.Ishiai,C.Wada,K.Miki

Key ref:

H.Komori et al. (1999). Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution. EMBO J, 18, 4597-4607. PubMed id: 10469640 DOI: 10.1093/emboj/18.17.4597

Date:

29-Apr-99 Release date: 09-Feb-00

Protein chain

P03856  (REPE1_ECOLI) -  Replication initiation protein from Escherichia coli (strain K12)

Seq: 251 a.a.

Struc: 214 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-C-T-G-T-G-A-C-A-A-A-T-T-G-C-C-C-T-C-A-G 21 bases

C-T-G-A-G-G-G-C-A-A-T-T-T-G-T-C-A-C-A-G-G 21 bases

DOI no: 10.1093/emboj/18.17.4597

EMBO J 18:4597-4607 (1999)

PubMed id: 10469640

Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution.

H.Komori, F.Matsunaga, Y.Higuchi, M.Ishiai, C.Wada, K.Miki.

ABSTRACT

The initiator protein (RepE) of F factor, a plasmid involved in sexual conjugation in Escherichia coli, has dual functions during the initiation of DNA replication which are determined by whether it exists as a dimer or as a monomer. A RepE monomer functions as a replication initiator, but a RepE dimer functions as an autogenous repressor. We have solved the crystal structure of the RepE monomer bound to an iteron DNA sequence of the replication origin of plasmid F. The RepE monomer consists of topologically similar N- and C-terminal domains related to each other by internal pseudo 2-fold symmetry, despite the lack of amino acid similarities between the domains. Both domains bind to the two major grooves of the iteron (19 bp) with different binding affinities. The C-terminal domain plays the leading role in this binding, while the N-terminal domain has an additional role in RepE dimerization. The structure also suggests that superhelical DNA induced at the origin of plasmid F by four RepEs and one HU dimer has an essential role in the initiation of DNA replication.

Selected figure(s)

Figure 1.
Figure 1 A schematic drawing of the functions of the RepE initiator protein in mini-F plasmid replication. The RepE monomers bind to the four iterons (direct repeats) of ori2 to initiate replication, whereas the RepE dimers bind to the inverted repeat of the repE promoter -operator to repress repE transcription. Parts of the repeated sequences (iterons) are shown at the top of the Figure where portions shared by the direct and inverted repeats are underlined (common 8 bp). The box indicates the RepE54 -iteron DNA complex determined in this study.

Figure 6.
Figure 6 (A) Positions of the conserved hydrophobic residues that form the hydrophobic core (in stereo). They are related by 2-fold symmetry, and the position of the 2-fold axis is indicated in black. (B) Polar interactions between the N- and C-terminal domains (in stereo). Arg37 in the 2 helix of the N-terminal domain interacts with the carbonyl oxygen of Lys155 in the 1' helix of the C-terminal domain. Arg167 in the 2' helix of the C-terminal domain interacts with the carbonyl oxygen of Ala27 in the 1' helix of the N-terminal domain. (C) Comparison of the DNA binding site sequences (iteron) of RepE and RepA initiator protein of pPS10 plasmid. Conserved sequences with their operator DNA sequence are boxed. The corresponding amino acid residues of RepE and RepA in contact with the bases on the DNA are indicated.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 4597-4607) copyright 1999.

Figures were selected by an automated process.