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6ozf

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Current revision (07:20, 11 October 2023) (edit) (undo)
 
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<StructureSection load='6ozf' size='340' side='right'caption='[[6ozf]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='6ozf' size='340' side='right'caption='[[6ozf]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6ozf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OZF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OZF FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6ozf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] 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=6OZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OZF 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.8&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene></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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nfi, TM_1865 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</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=6ozf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ozf OCA], [https://pdbe.org/6ozf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ozf RCSB], [https://www.ebi.ac.uk/pdbsum/6ozf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ozf ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </span></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=6ozf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ozf OCA], [http://pdbe.org/6ozf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ozf RCSB], [http://www.ebi.ac.uk/pdbsum/6ozf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ozf ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/NFI_THEMA NFI_THEMA]] Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Acts in DNA repair. In vitro, can also cleave single-stranded substrates with inosine, double-stranded DNA with apurinic sites, or DNA sites with uracil or a mismatched base. When present in molar excess, two protein molecules can bind to the same DNA substrate and effect cleavage of both strands (in vitro).<ref>PMID:12081482</ref>
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[https://www.uniprot.org/uniprot/NFI_THEMA NFI_THEMA] Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Acts in DNA repair. In vitro, can also cleave single-stranded substrates with inosine, double-stranded DNA with apurinic sites, or DNA sites with uracil or a mismatched base. When present in molar excess, two protein molecules can bind to the same DNA substrate and effect cleavage of both strands (in vitro).<ref>PMID:12081482</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
</div>
<div class="pdbe-citations 6ozf" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 6ozf" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 43589]]
 
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[[Category: Deoxyribonuclease V]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Samara, N L]]
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[[Category: Synthetic construct]]
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[[Category: Yang, W]]
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[[Category: Thermotoga maritima]]
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[[Category: Adenosine deamination]]
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[[Category: Samara NL]]
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[[Category: Dna damage]]
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[[Category: Yang W]]
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[[Category: Hydrolase]]
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[[Category: Metal ion dependent catalysis]]
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[[Category: Nucleic acid hydrolysis]]
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[[Category: Rna recognition]]
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Current revision

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

PDB ID 6ozf

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