9c64: Difference between revisions

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'''Unreleased structure'''


The entry 9c64 is ON HOLD  until Paper Publication
==Cytidine deaminase T6S toxin from Pseudomonas syringae complexed with substrate DNA==
<StructureSection load='9c64' size='340' side='right'caption='[[9c64]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9c64]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_syringae Pseudomonas syringae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9C64 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9C64 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]] 1.94&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IAS:BETA-L-ASPARTIC+ACID'>IAS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=9c64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9c64 OCA], [https://pdbe.org/9c64 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9c64 RCSB], [https://www.ebi.ac.uk/pdbsum/9c64 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9c64 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0A0Q0DAS4_PSEAP A0A0Q0DAS4_PSEAP]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA deaminase toxins are involved in interbacterial antagonism and the generation of genetic diversity in surviving bacterial populations. These enzymes have also been adopted as genome engineering tools. The single-stranded (ss)DNA deaminase SsdA is representative of the bacterial deaminase toxin family-2 (BaDTF2), and it deaminates ssDNA cytosines without a strong sequence context dependence, which contrasts with the AID/APOBEC family of sequence-selective ssDNA cytosine deaminases. Here we report the crystal structure of SsdA in complex with a ssDNA substrate. The structure reveals a unique mode of substrate binding, in which a cluster of aromatic residues engages ssDNA in a V-shaped conformation sharply bent across the target cytosine. The bases 5' or 3' to the target cytosine are stacked linearly and make mostly sequence non-specific protein contacts, thus explaining the broad substrate selectivity of SsdA. Unexpectedly, SsdA contains a beta-amino acid isoaspartate, which is important for enzymatic activity and contributes to the stability of SsdA as a toxin. Structure-function studies helped to design SsdA mutants active in human cells, which could lead to future applications in genome engineering.


Authors:  
Structural basis for sequence context-independent single-stranded DNA cytosine deamination by the bacterial toxin SsdA.,Yin L, Chen Y, Shi K, Barreto Duran E, Harris RS, Aihara H Nat Commun. 2025 Oct 3;16(1):8841. doi: 10.1038/s41467-025-63943-9. PMID:41044082<ref>PMID:41044082</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 9c64" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas syringae]]
[[Category: Aihara H]]
[[Category: Shi K]]
[[Category: Yin L]]
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