4ceh: Difference between revisions

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<StructureSection load='4ceh' size='340' side='right'caption='[[4ceh]], [[Resolution|resolution]] 3.24&Aring;' scene=''>
<StructureSection load='4ceh' size='340' side='right'caption='[[4ceh]], [[Resolution|resolution]] 3.24&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4ceh]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CEH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CEH FirstGlance]. <br>
<table><tr><td colspan='2'>[[4ceh]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168] 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=4CEH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CEH FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4cei|4cei]], [[4cej|4cej]]</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=4ceh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ceh OCA], [https://pdbe.org/4ceh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ceh RCSB], [https://www.ebi.ac.uk/pdbsum/4ceh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ceh ProSAT]</span></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=4ceh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ceh OCA], [http://pdbe.org/4ceh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ceh RCSB], [http://www.ebi.ac.uk/pdbsum/4ceh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ceh ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/ADDA_BACSU ADDA_BACSU]] An essential component of the DNA double-stranded break repair machinery, the heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the B.subtilis chi site (5'-AGCGG-3') which transforms the enzyme from a helicase which degrades both DNA strands to one with only 5' -> 3' exonuclease activity. This generates a double-stranded DNA with a protruding 3'-terminated single-stranded tail suitable for the initiation of homologous recombination (chi fragment). The AddA nuclease domain in particular is required for chi fragment generation; this subunit has 3' -> 5' nuclease and helicase activity. RecA thread formation during DNA double-strand break repair requires RecJ or AddAB.<ref>PMID:8387145</ref> <ref>PMID:10756102</ref> <ref>PMID:17570399</ref>  [[http://www.uniprot.org/uniprot/ADDB_BACSU ADDB_BACSU]] The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent single-stranded exonuclease, acting in both directions. Recognizes the B.subtilis chi site (5'-AGCGG-3') which transforms the enzyme from a helicase which degrades both DNA strands to one with only 5' to 3' exonuclease activity. This generates a double-stranded DNA with a protruding 3'-terminated single-stranded tail suitable for the initiation of homologous recombination (chi fragment). The AddB nuclease domain is not required for chi fragment generation; this subunit has 5' -> 3' nuclease activity. RecA thread formation during DNA double-strand break repair requires RecJ or AddAB.<ref>PMID:8387145</ref> <ref>PMID:10756102</ref> <ref>PMID:17570399</ref> 
[[https://www.uniprot.org/uniprot/ADDA_BACSU ADDA_BACSU]] An essential component of the DNA double-stranded break repair machinery, the heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the B.subtilis chi site (5'-AGCGG-3') which transforms the enzyme from a helicase which degrades both DNA strands to one with only 5' -> 3' exonuclease activity. This generates a double-stranded DNA with a protruding 3'-terminated single-stranded tail suitable for the initiation of homologous recombination (chi fragment). The AddA nuclease domain in particular is required for chi fragment generation; this subunit has 3' -> 5' nuclease and helicase activity. RecA thread formation during DNA double-strand break repair requires RecJ or AddAB.<ref>PMID:8387145</ref> <ref>PMID:10756102</ref> <ref>PMID:17570399</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence chi (Chi) and is catalysed by either an AddAB- or RecBCD-type helicase-nuclease (reviewed in refs 3, 4). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a chi sequence, whereupon they produce a 3' single-stranded DNA tail onto which they initiate loading of the RecA protein. Consequently, regulation of the AddAB/RecBCD complex by chi is a key control point in DNA repair and other processes involving genetic recombination. Here we report crystal structures of Bacillus subtilis AddAB in complex with different chi-containing DNA substrates either with or without a non-hydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, suggests how the enzyme binds specifically to chi sequences, and explains how chi recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single-molecule experiments.
 
Structural basis for translocation by AddAB helicase-nuclease and its arrest at chi sites.,Krajewski WW, Fu X, Wilkinson M, Cronin NB, Dillingham MS, Wigley DB Nature. 2014 Mar 16. doi: 10.1038/nature13037. PMID:24670664<ref>PMID:24670664</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4ceh" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacsu]]
[[Category: Bacillus subtilis subsp. subtilis str. 168]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cronin, N B]]
[[Category: Synthetic construct]]
[[Category: Fu, X]]
[[Category: Cronin NB]]
[[Category: Krajewski, W W]]
[[Category: Fu X]]
[[Category: Wigley, D]]
[[Category: Krajewski WW]]
[[Category: Wilkinson, M]]
[[Category: Wigley D]]
[[Category: Bacterial protein]]
[[Category: Wilkinson M]]
[[Category: Binding site]]
[[Category: Dna break]]
[[Category: Dna helicase]]
[[Category: Dna repair]]
[[Category: Dna- binding protein]]
[[Category: Double-stranded]]
[[Category: Exodeoxyribonuclease]]
[[Category: Exodeoxyribonuclease v]]
[[Category: Helicase-nuclease]]
[[Category: Homologous recombination]]
[[Category: Hydrolase-dna complex]]

Revision as of 20:41, 7 September 2022

Crystal structure of AddAB with a forked DNA substrateCrystal structure of AddAB with a forked DNA substrate

Structural highlights

4ceh is a 3 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ADDA_BACSU] An essential component of the DNA double-stranded break repair machinery, the heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the B.subtilis chi site (5'-AGCGG-3') which transforms the enzyme from a helicase which degrades both DNA strands to one with only 5' -> 3' exonuclease activity. This generates a double-stranded DNA with a protruding 3'-terminated single-stranded tail suitable for the initiation of homologous recombination (chi fragment). The AddA nuclease domain in particular is required for chi fragment generation; this subunit has 3' -> 5' nuclease and helicase activity. RecA thread formation during DNA double-strand break repair requires RecJ or AddAB.[1] [2] [3]

References

  1. ↑ Kooistra J, Haijema BJ, Venema G. The Bacillus subtilis addAB genes are fully functional in Escherichia coli. Mol Microbiol. 1993 Mar;7(6):915-23. PMID:8387145
  2. ↑ Chedin F, Ehrlich SD, Kowalczykowski SC. The Bacillus subtilis AddAB helicase/nuclease is regulated by its cognate Chi sequence in vitro. J Mol Biol. 2000 Apr 21;298(1):7-20. PMID:10756102 doi:http://dx.doi.org/10.1006/jmbi.2000.3556
  3. ↑ Yeeles JT, Dillingham MS. A dual-nuclease mechanism for DNA break processing by AddAB-type helicase-nucleases. J Mol Biol. 2007 Aug 3;371(1):66-78. Epub 2007 May 25. PMID:17570399 doi:http://dx.doi.org/10.1016/j.jmb.2007.05.053

4ceh, resolution 3.24Å

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