4U87

Crystal structure of the Ba-soaked C2 crystal form of pMV158 replication initiator RepB (P3221 space group)

Summary for 4U87

• Entry DOI: 10.2210/pdb4u87/pdb
• Related: 3DKX 3DKY
• Descriptor: Replication protein RepB, CHLORIDE ION, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: dna replication initiator, replication
• Biological source: Streptococcus agalactiae
• Total number of polymer chains: 3
• Total formula weight: 74368.43

Authors

Boer, D.R.,Ruiz Maso, J.A.,del Solar, G.,Coll, M. (deposition date: 2014-08-01, release date: 2015-08-26, Last modification date: 2023-12-20)

Primary citation

Boer, D.R.,Ruiz-Maso, J.A.,Rueda, M.,Petoukhov, M.V.,Machon, C.,Svergun, D.I.,Orozco, M.,Del Solar, G.,Coll, M.
Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158.
Sci Rep, 6:20915-20915, 2016

PubMed Abstract: DNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 is a hexameric ring protein evolutionary related to viral initiators. Here we explore the conformational plasticity of the RepB hexamer by i) SAXS, ii) sedimentation experiments, iii) molecular simulations and iv) X-ray crystallography. Combining these techniques, we derive an estimate of the conformational ensemble in solution showing that the C-terminal oligomerisation domains of the protein form a rigid cylindrical scaffold to which the N-terminal DNA-binding/catalytic domains are attached as highly flexible appendages, featuring multiple orientations. In addition, we show that the hinge region connecting both domains plays a pivotal role in the observed plasticity. Sequence comparisons and a literature survey show that this hinge region could exists in other initiators, suggesting that it is a common, crucial structural element for DNA binding and manipulation.

PubMed: 26875695
DOI: 10.1038/srep20915

Experimental method

X-RAY DIFFRACTION (3.8 Å)