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5fbb

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==S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate==
==S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate==
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<StructureSection load='5fbb' size='340' side='right' caption='[[5fbb]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
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<StructureSection load='5fbb' size='340' side='right'caption='[[5fbb]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5fbb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FBB FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5fbb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae_RIB40 Aspergillus oryzae RIB40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FBB 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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ETE:2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>ETE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.75&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5fb9|5fb9]], [[5fba|5fba]], [[5fbc|5fbc]], [[5fbd|5fbd]], [[5fbf|5fbf]], [[5fbg|5fbg]]</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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ETE:2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>ETE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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/Aspergillus_nuclease_S(1) Aspergillus nuclease S(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.30.1 3.1.30.1] </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=5fbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fbb OCA], [https://pdbe.org/5fbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fbb RCSB], [https://www.ebi.ac.uk/pdbsum/5fbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fbb 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=5fbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fbb OCA], [http://pdbe.org/5fbb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fbb RCSB], [http://www.ebi.ac.uk/pdbsum/5fbb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fbb ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/NUS1_ASPOR NUS1_ASPOR]] Hydrolyzes only single-stranded DNA and RNA without apparent specificity for bases.
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[https://www.uniprot.org/uniprot/NUS1_ASPOR NUS1_ASPOR] Hydrolyzes only single-stranded DNA and RNA without apparent specificity for bases.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.
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Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.,Koval T, Ostergaard LH, Lehmbeck J, Norgaard A, Lipovova P, Duskova J, Skalova T, Trundova M, Kolenko P, Fejfarova K, Stransky J, Svecova L, Hasek J, Dohnalek J PLoS One. 2016 Dec 30;11(12):e0168832. doi: 10.1371/journal.pone.0168832., eCollection 2016. PMID:28036383<ref>PMID:28036383</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 5fbb" 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: Dohnalek, J]]
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[[Category: Aspergillus oryzae RIB40]]
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[[Category: Koval, T]]
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[[Category: Large Structures]]
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[[Category: Oestergaard, L H]]
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[[Category: Dohnalek J]]
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[[Category: Complex]]
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[[Category: Koval T]]
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[[Category: Endonuclease]]
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[[Category: Oestergaard LH]]
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[[Category: Hydrolase]]
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[[Category: Zinc dependent]]
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Current revision

S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate

PDB ID 5fbb

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