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1ak0

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(New page: 200px<br /><applet load="1ak0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ak0, resolution 1.8&Aring;" /> '''P1 NUCLEASE IN COMPLE...)
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[[Image:1ak0.gif|left|200px]]<br /><applet load="1ak0" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ak0, resolution 1.8&Aring;" />
 
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'''P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG'''<br />
 
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==Overview==
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==P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG==
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The reaction mechanism of nuclease P1 from Penicillium citrinum has been, investigated using single-stranded dithiophosphorylated di-, tetra-, and, hexanucleotides as substrate analogs. The complexes crystallize in, tetragonal and orthorhombic space groups and have been solved by molecular, replacement. The high resolution structures give a clear picture of base, recognition by P1 nuclease at its two nucleotide-binding sites, especially, the 1.8 A structure of a P1-tetranucleotide complex which can be, considered a P1-product complex. The observed binding modes are in, agreement with a catalytic mechanism where the two closely spaced zinc, ions activate the attacking water while the third, more exposed zinc ion, stabilizes the leaving 03' oxyanion. Stacking as well as hydrogen bonding, interactions with the base 5' to the cleaved phosphodiester bond are, important elements of substrate binding and recognition. Modelling of a, productive P1-substrate complex based on the solved structures suggests, steric hindrance as the likely reason for the resistance of, Rp-phosphorothioates and phosphorodithioates. Differences with the highly, homologous nuclease S1 from Aspergillus oryzae are discussed.
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<StructureSection load='1ak0' size='340' side='right'caption='[[1ak0]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1ak0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_citrinum Penicillium citrinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AK0 FirstGlance]. <br>
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1AK0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_citrinum Penicillium citrinum] with NAG, ZN and ADS as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AK0 OCA].
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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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADS:ADENOSINE-5-(DITHIO)PHOSPHATE'>ADS</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=THS:THYMIDINE-5-(DITHIO)PHOSPHATE'>THS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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==Reference==
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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=1ak0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ak0 OCA], [https://pdbe.org/1ak0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ak0 RCSB], [https://www.ebi.ac.uk/pdbsum/1ak0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ak0 ProSAT]</span></td></tr>
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Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs., Romier C, Dominguez R, Lahm A, Dahl O, Suck D, Proteins. 1998 Sep 1;32(4):414-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9726413 9726413]
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</table>
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[[Category: Aspergillus nuclease S(1)]]
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== Function ==
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[https://www.uniprot.org/uniprot/NUP1_PENCI NUP1_PENCI] Hydrolyzes only single-stranded DNA and RNA without apparent specificity for bases.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/1ak0_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ak0 ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Penicillium citrinum]]
[[Category: Penicillium citrinum]]
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[[Category: Single protein]]
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[[Category: Romier C]]
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[[Category: Romier, C.]]
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[[Category: Suck D]]
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[[Category: Suck, D.]]
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[[Category: ADS]]
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[[Category: NAG]]
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[[Category: ZN]]
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[[Category: endonuclease]]
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[[Category: glycosylated protein]]
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[[Category: p1 nuclease]]
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[[Category: reaction mechanism]]
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[[Category: thiophosphorylated oligonucleotides]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:54:53 2007''
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Current revision

P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG

PDB ID 1ak0

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