3dky | pdb_00003dky

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

spinqualitylabelsall models 3dky, resolution 3.60Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3dky is a 6 chain structure with sequence from Streptococcus agalactiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.6Å Ligands: MN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function REPB_STRAG Is essential for plasmid replication. Nicks the positive strand at the plus origin of replication. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains.,Boer DR, Ruiz-Maso JA, Lopez-Blanco JR, Blanco AG, Vives-Llacer M, Chacon P, Uson I, Gomis-Ruth FX, Espinosa M, Llorca O, del Solar G, Coll M EMBO J. 2009 Jun 3;28(11):1666-78. PMID:19440202 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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