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4pbb

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==The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI==
==The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI==
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<StructureSection load='4pbb' size='340' side='right' caption='[[4pbb]], [[Resolution|resolution]] 3.46&Aring;' scene=''>
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<StructureSection load='4pbb' size='340' side='right'caption='[[4pbb]], [[Resolution|resolution]] 3.46&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4pbb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PBB FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4pbb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii_SDF Acinetobacter baumannii SDF]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PBB FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.46&#8491;</td></tr>
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<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=4pbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pbb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pbb RCSB], [http://www.ebi.ac.uk/pdbsum/4pbb PDBsum]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4pbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pbb OCA], [https://pdbe.org/4pbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pbb RCSB], [https://www.ebi.ac.uk/pdbsum/4pbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pbb ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/B0VN39_ACIBS B0VN39_ACIBS]
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AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves deoxyribonucleic acid (DNA) containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI has been used as a tool for mapping the genomic locations of 5hmC, an important epigenetic modification in the DNA of higher organisms. Here we report the crystal structures of AbaSI in the presence and absence of DNA. These structures provide considerable, although incomplete, insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal helices mediate most of the homodimer interface. Dimerization brings together the two catalytic sites required for double-strand cleavage, and separates the 5hmC binding-domains by approximately 70 A, consistent with the known activity of AbaSI which cleaves DNA optimally between symmetrically modified cytosines approximately 22 bp apart. The eukaryotic SET and RING-associated (SRA) domains bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG sequence. They make contacts in both the major and minor DNA grooves, and flip the modified cytosine out of the helix into a conserved binding pocket. In contrast, the SRA-like domain of AbaSI, which has no sequence specificity, contacts only the minor DNA groove, and in our current structures the 5hmC remains intra-helical. A conserved, binding pocket is nevertheless present in this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely, therefore, that base-flipping is part of the recognition and cleavage mechanism of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior to actual recognition.
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Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA.,Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S, Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X Nucleic Acids Res. 2014 Jun 3. pii: gku497. PMID:24895434<ref>PMID:24895434</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Cheng, X]]
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[[Category: Acinetobacter baumannii SDF]]
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[[Category: Horton, J R]]
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[[Category: Large Structures]]
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[[Category: Epigenetic sequencing tool]]
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[[Category: Cheng X]]
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[[Category: Hydrolase]]
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[[Category: Horton JR]]
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[[Category: Hydroxymethylcytosine-dependent restriction enzyme]]
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[[Category: Sra domain-like]]
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[[Category: Vsr endonuclease-like]]
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Current revision

The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI

PDB ID 4pbb

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