Dataset Information

A structural basis for the regulatory inactivation of DnaA.

ABSTRACT: Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.

SUBMITTER: Xu Q

PROVIDER: S-EPMC2667141 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A structural basis for the regulatory inactivation of DnaA.

Xu Qingping Q McMullan Daniel D Abdubek Polat P Astakhova Tamara T Carlton Dennis D Chen Connie C Chiu Hsiu-Ju HJ Clayton Thomas T Das Debanu D Deller Marc C MC Duan Lian L Elsliger Marc-Andre MA Feuerhelm Julie J Hale Joanna J Han Gye Won GW Jaroszewski Lukasz L Jin Kevin K KK Johnson Hope A HA Klock Heath E HE Knuth Mark W MW Kozbial Piotr P Sri Krishna S S Kumar Abhinav A Marciano David D Miller Mitchell D MD Morse Andrew T AT Nigoghossian Edward E Nopakun Amanda A Okach Linda L Oommachen Silvya S Paulsen Jessica J Puckett Christina C Reyes Ron R Rife Christopher L CL Sefcovic Natasha N Trame Christine C van den Bedem Henry H Weekes Dana D Hodgson Keith O KO Wooley John J Deacon Ashley M AM Godzik Adam A Lesley Scott A SA Wilson Ian A IA

Journal of molecular biology 20081030 2

Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the ...[more]

PMID: 19000695

Similar Datasets

Project description:The coupled interplay between activation and inactivation gating is a functional hallmark of K(+) channels. This coupling has been experimentally demonstrated through ion interaction effects and cysteine accessibility, and is associated with a well defined boundary of energetically coupled residues. The structure of the K(+) channel KcsA in its fully open conformation, in addition to four other partial channel openings, richly illustrates the structural basis of activation-inactivation gating. Here, we identify the mechanistic principles by which movements on the inner bundle gate trigger conformational changes at the selectivity filter, leading to the non-conductive C-type inactivated state. Analysis of a series of KcsA open structures suggests that, as a consequence of the hinge-bending and rotation of the TM2 helix, the aromatic ring of Phe 103 tilts towards residues Thr 74 and Thr 75 in the pore-helix and towards Ile 100 in the neighbouring subunit. This allows the network of hydrogen bonds among residues Trp 67, Glu 71 and Asp 80 to destabilize the selectivity filter, allowing entry to its non-conductive conformation. Mutations at position 103 have a size-dependent effect on gating kinetics: small side-chain substitutions F103A and F103C severely impair inactivation kinetics, whereas larger side chains such as F103W have more subtle effects. This suggests that the allosteric coupling between the inner helical bundle and the selectivity filter might rely on straightforward mechanical deformation propagated through a network of steric contacts. Average interactions calculated from molecular dynamics simulations show favourable open-state interaction-energies between Phe 103 and the surrounding residues. We probed similar interactions in the Shaker K(+) channel where inactivation was impaired in the mutant I470A. We propose that side-chain rearrangements at position 103 mechanically couple activation and inactivation in KcsA and a variety of other K(+) channels.

Dataset Information

A structural basis for the regulatory inactivation of DnaA.

Publications

A structural basis for the regulatory inactivation of DnaA.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets