PDBsum entry 1l8q

DNA binding protein

PDB id: 1l8q

Contents

Protein chain

321 a.a. *

Ligands

ADP

Metals

_MG

Waters ×47

* Residue conservation analysis

PDB id:

1l8q

Name:

DNA binding protein

Title:

Crystal structure of DNA replication initiation factor

Structure:

Chromosomal replication initiator protein dnaa. Chain: a. Fragment: residues 76-399. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: dnaa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.231 R-free: 0.255

Authors:

J.P.Erzberger,M.M.Pirruccello,J.M.Berger

Key ref:

J.P.Erzberger et al. (2002). The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J, 21, 4763-4773. PubMed id: 12234917 DOI: 10.1093/emboj/cdf496

Date:

21-Mar-02 Release date: 25-Sep-02

Protein chain

O66659  (DNAA_AQUAE) -  Chromosomal replication initiator protein DnaA from Aquifex aeolicus (strain VF5)

Seq: 399 a.a.

Struc: 321 a.a.

DOI no: 10.1093/emboj/cdf496

EMBO J 21:4763-4773 (2002)

PubMed id: 12234917

The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation.

J.P.Erzberger, M.M.Pirruccello, J.M.Berger.

ABSTRACT

The initiation of DNA replication is a key event in the cell cycle of all organisms. In bacteria, replication initiation occurs at specific origin sequences that are recognized and processed by an oligomeric complex of the initiator protein DnaA. We have determined the structure of the conserved core of the Aquifex aeolicus DnaA protein to 2.7 A resolution. The protein comprises an AAA+ nucleotide-binding fold linked through a long, helical connector to an all-helical DNA-binding domain. The structure serves as a template for understanding the physical consequences of a variety of DnaA mutations, and conserved motifs in the protein suggest how two critical aspects of origin processing, DNA binding and homo-oligomerization, are mediated. The spatial arrangement of these motifs in DnaA is similar to that of the eukaryotic-like archaeal replication initiation factor Cdc6/Orc1, demonstrating that mechanistic elements of origin processing may be conserved across bacterial, archaeal and eukaryotic domains of life.

Selected figure(s)

Figure 3.
Figure 3 (A) RIBBONS diagram highlighting the position of E.coli DnaA mutations mapped to the A.aeolicus DnaA model (blue spheres). Identification and phenotype of mutations can be found in Table II. The shaded oval (gray) marks the location of the 12 hinge region reported to play a role in cardiolipin-mediated effects. (B) RIBBONS diagrams of DnaA domain IV and trp repressor DNA-binding domain/DNA complex (Otwinowski et al., 1988) highlighting the closely related HTH motif in gold. Highly conserved residues in the basic loop and the DnaA signature sequences are indicated by spheres. Residues determined by mutagenesis to be critical for DNA binding in E.coli that map to the HTH and the basic loop motifs are highlighted in red. (C) RIBBONS model of the DnaA−DNA complex based on the trp repressor/DNA complex. The positions of the signature sequence motif and the basic loop are indicated.

Figure 4.
Figure 4 (A) RIBBONS diagram of DnaA and p97 (residues 191−458) showing the high degree of structural conservation across the AAA+ domain of the two proteins (the r.m.s.d. between the two proteins is 3.2 Å over 192 C[ ]positions). (B) RIBBONS diagram of the AAA+ region of a p97 dimer excised from the hexameric structure (inset) (Zhang et al., 2000) depicting the typical oligomeric arrangement of AAA+ protomers. The ADP bound at the interface is shown in black. The helix containing the Box VII motif is shown in cyan and the key arginine residue present at the dimerization interface is depicted as a magenta ball-and-stick model. (C) Inset: surface depiction (Nicholls et al., 1991) of the DnaA dimer modeled on p97, showing the high degree of complementarity between the monomers. The structural alignment of the AAA+ regions was generated using least-squares fitting of the DnaA AAA+ domain on each of two neighboring p97 AAA+ domains from the p97 hexamer. The exploded view reveals the clustering of conserved residues at the dimerization interface to form the bipartite nucleotide-interaction site. The degree of conservation among all known DnaA sequences is indicated by the degree of blue shading (Figure 1B); invariant (magenta) and chemically conserved residues (pink) are also highlighted. (D) RIBBONS diagram of the DnaA AAA+ domain (residues D77^S130−G290^N348) model dimer shown in blue and gold. Critical elements present at the predicted dimer interface are highlighted as in Figure 4B.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 4763-4773) copyright 2002.

Figures were selected by an automated process.