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4rd5

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==Crystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate DNA==
==Crystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate DNA==
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<StructureSection load='4rd5' size='340' side='right' caption='[[4rd5]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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<StructureSection load='4rd5' size='340' side='right'caption='[[4rd5]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4rd5]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Neig1 Neig1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RD5 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4rd5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_gonorrhoeae_FA_1090 Neisseria gonorrhoeae FA 1090]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RD5 FirstGlance]. <br>
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</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NGO0364 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=242231 NEIG1])</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]] 2.7&#8491;</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/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></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=4rd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rd5 OCA], [https://pdbe.org/4rd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rd5 RCSB], [https://www.ebi.ac.uk/pdbsum/4rd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rd5 ProSAT]</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=4rd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rd5 OCA], [http://pdbe.org/4rd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rd5 RCSB], [http://www.ebi.ac.uk/pdbsum/4rd5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rd5 ProSAT]</span></td></tr>
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</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/Q5F9M9_NEIG1 Q5F9M9_NEIG1]
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The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al., 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and in plant transcription factors. Structural comparison of the B3-like domains of R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved DNA-binding surface comprised of N- and C-arms that together grip the DNA. The C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but the R.NgoAVII N-arm which makes the majority of the contacts to the target site is much longer. The overall structures of R.NgoAVII and BfiI are similar; however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at the target site. The structures we present will help formulate future experiments to explore the molecular mechanisms of intersubunit crosstalk that control DNA cleavage by R.NgoAVII and related endonucleases.
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Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII.,Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V Nucleic Acids Res. 2014 Dec 16;42(22):14022-30. doi: 10.1093/nar/gku1237. Epub, 2014 Nov 27. PMID:25429979<ref>PMID:25429979</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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<div class="pdbe-citations 4rd5" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Neig1]]
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[[Category: Large Structures]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Neisseria gonorrhoeae FA 1090]]
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[[Category: Grazulis, S]]
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[[Category: Grazulis S]]
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[[Category: Siksnys, V]]
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[[Category: Siksnys V]]
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[[Category: Silanskas, A]]
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[[Category: Silanskas A]]
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[[Category: Tamulaitiene, G]]
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[[Category: Tamulaitiene G]]
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[[Category: Zaremba, M]]
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[[Category: Zaremba M]]
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[[Category: B3 dna binding domain]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Protein-dna complex]]
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[[Category: Restriction endonuclease]]
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Current revision

Crystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate DNA

PDB ID 4rd5

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