5fdk: Difference between revisions

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-'''Unreleased structure'''
-The entry 5fdk is ON HOLD  until Paper Publication
+==Crystal structure of RecU(D88N) in complex with palindromic DNA duplex==
+<StructureSection load='5fdk' size='340' side='right'caption='[[5fdk]], [[Resolution|resolution]] 3.21&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5fdk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FDK FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.208&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5fdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fdk OCA], [https://pdbe.org/5fdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fdk RCSB], [https://www.ebi.ac.uk/pdbsum/5fdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fdk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RECU_BACSU RECU_BACSU] Has at least 2 separable functions; Holliday junction resolution with generation of monomeric chromosomes, and modulation of RecA activity. Endonuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves mobile four-strand junctions by introducing symmetrical nicks in paired strands. Promotes annealing of linear ssDNA with homologous dsDNA. Required for DNA repair, homologous recombination and chromosome segregation. Partially inhibits the hydrolysis of dATP or rATP by RecA. Holliday junction resolution is stimulated by RuvB.<ref>PMID:14701911</ref> <ref>PMID:16020779</ref> <ref>PMID:16154091</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 A. This structure shows the stalk region and the essential N-terminal region (NTR) previously unseen in our DNA unbound structure. The flexible nature of the NTR in solution was confirmed using SAXS. Thermofluor studies performed to assess the stability of RecU in complex with the arms of an HJ indicate that it confers stability. Further, we performed molecular dynamics (MD) simulations of wild type and an NTR deletion variant of RecU, with and without HJ. The NTR is observed to be highly flexible in simulations of the unbound RecU, in agreement with SAXS observations. These simulations revealed domain dynamics of RecU and their role in the formation of complex with HJ. The MD simulations also elucidate key roles of the NTR, stalk region, and breathing motion of RecU in the formation of the reactive state.
-Authors: Khavnekar, S., Rafferty, J.B., Kale, A.
+Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state.,Khavnekar S, Dantu SC, Sedelnikova S, Ayora S, Rafferty J, Kale A Nucleic Acids Res. 2016 Nov 29. pii: gkw1165. PMID:27903910<ref>PMID:27903910</ref>
-Description: Crystal structure of RecU(D88N) in complex with palindromic DNA duplex
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Khavnekar, S]]
+<div class="pdbe-citations 5fdk" style="background-color:#fffaf0;"></div>
-[[Category: Kale, A]]
-[[Category: Rafferty, J.B]]
+==See Also==
+*[[Resolvase 3D structures|Resolvase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bacillus subtilis]]
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Kale A]]
+[[Category: Khavnekar S]]
+[[Category: Rafferty JB]]