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| | <StructureSection load='4oky' size='340' side='right'caption='[[4oky]], [[Resolution|resolution]] 2.90Å' scene=''> | | <StructureSection load='4oky' size='340' side='right'caption='[[4oky]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4oky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29905 Atcc 29905]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OKY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4oky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OKY FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pvuRts1I ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585 ATCC 29905])</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=4oky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oky OCA], [https://pdbe.org/4oky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oky RCSB], [https://www.ebi.ac.uk/pdbsum/4oky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oky 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=4oky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oky OCA], [http://pdbe.org/4oky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oky RCSB], [http://www.ebi.ac.uk/pdbsum/4oky PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oky ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q52612_PROVU Q52612_PROVU] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 29905]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Shao, C]] | + | [[Category: Proteus vulgaris]] |
| - | [[Category: Wang, C L]] | + | [[Category: Shao C]] |
| - | [[Category: Zang, J Y]] | + | [[Category: Wang CL]] |
| - | [[Category: Dna binding protein]] | + | [[Category: Zang JY]] |
| - | [[Category: Restriction endonuclease]]
| + | |
| - | [[Category: Sra-like domain]]
| + | |
| Structural highlights
Function
Q52612_PROVU
Publication Abstract from PubMed
5-Hydroxymethylation is a curious modification of cytosine that was discovered some decades ago, but its functional role in eukaryotes still awaits elucidation. 5-Hydroxymethylcytosine is an epigenetic marker that is crucial for multiple biological processes. The profile is altered under certain disease conditions such as cancer, Huntington's disease and Alzheimer's disease. Using the DNA-modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq), the hydroxymethylome can be deciphered at the resolution of individual bases. The method is based on the enzymatic properties of AbaSI, a member of the PvuRts1I family of endonucleases. PvuRts1I is a modification-dependent endonuclease with high selectivity for 5-hydroxymethylcytosine over 5-methylcytosine and cytosine. In this study, the crystal structure of PvuRts1I was determined in order to understand and improve the substrate selectivity. A nuclease domain and an SRA-like domain are located at the N- and C-termini, respectively. Through comparison with other SRA-domain structures, the SRA-like domain was proposed to be the 5-hmC recognition module. Several mutants of PvuRts1I with enzymatic activity restricted to 5-hydroxymethylcytosine only were generated based on the structural analysis, and these enzyme variants are appropriate for separating the hydroxymethylome from the wider methylome.
Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease.,Shao C, Wang C, Zang J Acta Crystallogr D Biol Crystallogr. 2014 Sep;70(Pt 9):2477-86. doi:, 10.1107/S139900471401606X. Epub 2014 Aug 29. PMID:25195760[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shao C, Wang C, Zang J. Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease. Acta Crystallogr D Biol Crystallogr. 2014 Sep;70(Pt 9):2477-86. doi:, 10.1107/S139900471401606X. Epub 2014 Aug 29. PMID:25195760 doi:http://dx.doi.org/10.1107/S139900471401606X
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