5fdk

From Proteopedia

(Difference between revisions)

Revision as of 07:13, 6 May 2020

Crystal structure of RecU(D88N) in complex with palindromic DNA duplex

Structural highlights

5fdk is a 8 chain structure with sequence from "vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1zp7
Gene:	recU, prfA, yppB, BSU22310 ("Vibrio subtilis" Ehrenberg 1835)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3]

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.

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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ayora S, Carrasco B, Doncel-Perez E, Lurz R, Alonso JC. Bacillus subtilis RecU protein cleaves Holliday junctions and anneals single-stranded DNA. Proc Natl Acad Sci U S A. 2004 Jan 13;101(2):452-7. Epub 2003 Dec 30. PMID:14701911 doi:http://dx.doi.org/10.1073/pnas.2533829100
↑ Sanchez H, Kidane D, Reed P, Curtis FA, Cozar MC, Graumann PL, Sharples GJ, Alonso JC. The RuvAB branch migration translocase and RecU Holliday junction resolvase are required for double-stranded DNA break repair in Bacillus subtilis. Genetics. 2005 Nov;171(3):873-83. Epub 2005 Jul 14. PMID:16020779 doi:http://dx.doi.org/genetics.105.045906
↑ McGregor N, Ayora S, Sedelnikova S, Carrasco B, Alonso JC, Thaw P, Rafferty J. The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage. Structure. 2005 Sep;13(9):1341-51. PMID:16154091 doi:10.1016/j.str.2005.05.011
↑ Khavnekar S, Dantu SC, Sedelnikova S, Ayora S, Rafferty J, Kale A. Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state. Nucleic Acids Res. 2016 Nov 29. pii: gkw1165. PMID:27903910 doi:http://dx.doi.org/10.1093/nar/gkw1165

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5fdk"

@@ Line 1: / Line 1: @@
 ==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=''>
+<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. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FDK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5fdk]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. 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 [http://proteopedia.org/fgij/fg.htm?mol=5FDK FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zp7|1zp7]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5fdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fdk OCA], [http://pdbe.org/5fdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fdk RCSB], [http://www.ebi.ac.uk/pdbsum/5fdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fdk ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">recU, prfA, yppB, BSU22310 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5fdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fdk OCA], [http://pdbe.org/5fdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fdk RCSB], [http://www.ebi.ac.uk/pdbsum/5fdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fdk ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 5fdk" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Resolvase 3D structures|Resolvase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Vibrio subtilis ehrenberg 1835]]
+[[Category: Large Structures]]
 [[Category: Kale, A]]
 [[Category: Khavnekar, S]]

5fdk

From Proteopedia

Revision as of 07:13, 6 May 2020

Crystal structure of RecU(D88N) in complex with palindromic DNA duplex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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