1skb: Difference between revisions

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-[[Image:1skb.png|left|200px]]
-{{STRUCTURE_1skb|  PDB=1skb  |  SCENE=  }}
+==Crystallographic snapshots of Aspergillus fumigatus phytase revealing its enzymatic dynamics==
+<StructureSection load='1skb' size='340' side='right'caption='[[1skb]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1skb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_fumigatus Aspergillus fumigatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SKB FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.58&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=1skb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skb OCA], [https://pdbe.org/1skb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1skb RCSB], [https://www.ebi.ac.uk/pdbsum/1skb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1skb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PHYA_ASPFU PHYA_ASPFU] Catalyzes the hydrolysis of inorganic orthophosphate from phytate.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sk/1skb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1skb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Understanding of the atomic movements involved in an enzymatic reaction needs structural information on the active and inactive native enzyme molecules and on the enzyme-substrate, enzyme-intermediate, and enzyme-product(s) complexes. By using the X-ray crystallographic method, four crystal structures of Aspergillus fumigatus phytase were obtained at resolution higher than 1.7 A. The pH-dependent catalytic activity of A. fumigatus phytase was linked to three water molecules that may prevent the substrate from binding and thus block nucleophilic attack of the catalytic imidazole nitrogen. Comparison of various structures also identified the water molecule that attacks the phosphamide bond during the hydrolysis process, and established the hydrolysis pathway of the intermediate. Additionally, two reaction product phosphates were observed at the active site, suggesting a possible product release pathway after hydrolysis of the intermediate. These results can help explain the catalytic mechanism throughout the whole acid phosphatase family, as all key residues are conserved.
-===Crystallographic snapshots of Aspergillus fumigatus phytase revealing its enzymatic dynamics===
+Crystallographic snapshots of Aspergillus fumigatus phytase, revealing its enzymatic dynamics.,Liu Q, Huang Q, Lei XG, Hao Q Structure. 2004 Sep;12(9):1575-83. PMID:15341723<ref>PMID:15341723</ref>
-{{ABSTRACT_PUBMED_15341723}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1skb" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[1skb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_fumigatus Aspergillus fumigatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SKB OCA].
+*[[Phytase 3D structures|Phytase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:015341723</ref><references group="xtra"/>
+__TOC__
-[[Category: 3-phytase]]
+</StructureSection>
 [[Category: Aspergillus fumigatus]]
-[[Category: Hao, Q.]]
+[[Category: Large Structures]]
-[[Category: Huang, Q.]]
+[[Category: Hao Q]]
-[[Category: Lei, X G.]]
+[[Category: Huang Q]]
-[[Category: Liu, Q.]]
+[[Category: Lei XG]]
-[[Category: Big alpha/beta domain]]
+[[Category: Liu Q]]
-[[Category: Catalytic dynamic]]
-[[Category: Catalytic site]]
-[[Category: Hydrolase]]
-[[Category: Product release pathway]]
-[[Category: Small alpha domain]]
-[[Category: Water structure]]