PDBsum entry 2hcb

Replication

PDB id: 2hcb

Contents

Protein chains

317 a.a. *

Ligands

ACP ×4

Metals

_MG ×4

* Residue conservation analysis

PDB id:

2hcb

Name:

Replication

Title:

Structure of amppcp-bound dnaa from aquifex aeolicus

Structure:

Chromosomal replication initiator protein dnaa. Chain: a, b, c, d. Engineered: yes

Source:

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

Resolution:

3.51Å R-factor: 0.267 R-free: 0.298

Authors:

J.P.Erzberger,M.L.Mott,J.M.Berger

Key ref:

J.P.Erzberger et al. (2006). Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Biol, 13, 676-683. PubMed id: 16829961 DOI: 10.1038/nsmb1115

Date:

15-Jun-06 Release date: 25-Jul-06

Protein chains

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

Seq: 399 a.a.

Struc: 317 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/nsmb1115

Nat Struct Biol 13:676-683 (2006)

PubMed id: 16829961

Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling.

J.P.Erzberger, M.L.Mott, J.M.Berger.

ABSTRACT

In bacteria, the initiation of replication is controlled by DnaA, a member of the ATPases associated with various cellular activities (AAA+) protein superfamily. ATP binding allows DnaA to transition from a monomeric state into a large oligomeric complex that remodels replication origins, triggers duplex melting and facilitates replisome assembly. The crystal structure of AMP-PCP-bound DnaA reveals a right-handed superhelix defined by specific protein-ATP interactions. The observed quaternary structure of DnaA, along with topology footprint assays, indicates that a right-handed DNA wrap is formed around the initiation nucleoprotein complex. This model clarifies how DnaA engages and unwinds bacterial origins and suggests that additional, regulatory AAA+ proteins engage DnaA at filament ends. Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly forms the core element of initiators in all domains of life.

Selected figure(s)

Figure 1.
Figure 1. Structure of ATP-DnaA. (a) Overlay of the four DnaA monomers in the asymmetric unit. The AAA+ module is colored green and red (domains IIIA and IIIB, respectively); domain IV, the DNA-binding element, is yellow. The ATP analog AMP-PCP is shown as black sticks. The helix-turn-helix (HTH) motif in domain IV and the N and C termini are labeled. (b) ATP-DnaA forms a right-handed helical filament with 8[1] symmetry. Side and axial views of four symmetry-related DnaA tetramers are shown. Top, the four monomers in the asymmetric unit are colored blue, green, orange and yellow. Bottom, identical view, but protomers are colored by domain as in a.

Figure 5.
Figure 5. Conformational changes induced by ATP binding. (a) ATP-DnaA dimer (blue and gold) with ADP-DnaA (green; PDB entry 1L8Q) superposed on one subunit. (b) Detail, with arrows indicating movement of the AAA+ lid (DnaA domain IIIB) required to accommodate a steric clash that occurs in the ADP-DnaA AAA+ orientation (red circle). (c) Stereo view of the molecular features of the ADP-to-ATP switch. The lid movement is stabilized by interactions of the sensor II (SII) arginine with the -phosphate and enables the box VII helix to engage the nucleotide through the arginine finger (Arg230). Further stability is provided by interactions of Glu280 with the ribose ring and of the box VII residue Ser229 with Arg277.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2006, 13, 676-683) copyright 2006.

Figures were selected by an automated process.