3DKY

Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), tetragonal form, to 3.6 Ang resolution

3DKY の概要

• エントリーDOI: 10.2210/pdb3dky/pdb
• 関連するPDBエントリー: 1ksx 1ksy 1l2m 1rz9 2gxa 2hw0 3DKX
• 分子名称: Replication protein repB, MANGANESE (II) ION (2 entities in total)
• 機能のキーワード: replication initiation, plasmid replication, nuclease, hexamer, flexible nuclease domains, dna replication, plasmid, replication initiator, replication
• 由来する生物種: Streptococcus agalactiae
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 145942.38

構造登録者

Boer, D.R.,Ruiz-Maso, J.A.,Blanco, A.G.,Vives-Llacer, M.,Uson, I.,Gomis-Ruth, F.X.,Espinosa, M.,Del Solar, G.,Coll, M. (登録日: 2008-06-26, 公開日: 2009-06-30, 最終更新日: 2023-11-01)

主引用文献

Boer, D.R.,Ruiz-Maso, J.A.,Lopez-Blanco, J.R.,Blanco, A.G.,Vives-Llacer, M.,Chacon, P.,Uson, I.,Gomis-Ruth, F.X.,Espinosa, M.,Llorca, O.,del Solar, G.,Coll, M.
Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains
Embo J., 28:1666-1678, 2009

PubMed Abstract: RepB initiates plasmid rolling-circle replication by binding to a triple 11-bp direct repeat (bind locus) and cleaving the DNA at a specific distant site located in a hairpin loop within the nic locus of the origin. The structure of native full-length RepB reveals a hexameric ring molecule, where each protomer has two domains. The origin-binding and catalytic domains show a three-layer alpha-beta-alpha sandwich fold. The active site is positioned at one of the faces of the beta-sheet and coordinates a Mn2+ ion at short distance from the essential nucleophilic Y99. The oligomerization domains (ODs), each consisting of four alpha-helices, together define a compact ring with a central channel, a feature found in ring helicases. The toroidal arrangement of RepB suggests that, similar to ring helicases, it encircles one of the DNA strands during replication to confer processivity to the replisome complex. The catalytic domains appear to be highly mobile with respect to ODs. This mobility may account for the adaptation of the protein to two distinct DNA recognition sites.

PubMed: 19440202
DOI: 10.1038/emboj.2009.125

実験手法

X-RAY DIFFRACTION (3.6 Å)