3DKX

Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), trigonal form, to 2.7 Ang resolution

Summary for 3DKX

• Entry DOI: 10.2210/pdb3dkx/pdb
• Related: 1ksx 1ksy 1l2m 1rz9 2gxa 2hw0 3DKY
• Descriptor: Replication protein repB, MANGANESE (II) ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: replication initiation, plasmid replication, nuclease, hexamer, flexible nuclease domains, dna replication, plasmid, replication initiator, replication
• Biological source: Streptococcus agalactiae
• Total number of polymer chains: 3
• Total formula weight: 73156.79

Authors

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. (deposition date: 2008-06-26, release date: 2009-06-30, Last modification date: 2024-03-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.7 Å)