1skb: Difference between revisions

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<StructureSection load='1skb' size='340' side='right'caption='[[1skb]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
<StructureSection load='1skb' size='340' side='right'caption='[[1skb]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1skb]] is a 1 chain structure. 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>
<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='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>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qwo|1qwo]], [[1sk8|1sk8]], [[1sk9|1sk9]], [[1ska|1ska]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-phytase 3-phytase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.8 3.1.3.8] </span></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>
<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>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PHYA_ASPFU PHYA_ASPFU]] Catalyzes the hydrolysis of inorganic orthophosphate from phytate.  
[https://www.uniprot.org/uniprot/PHYA_ASPFU PHYA_ASPFU] Catalyzes the hydrolysis of inorganic orthophosphate from phytate.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1skb ConSurf].
</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="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.,Liu Q, Huang Q, Lei XG, Hao Q Structure. 2004 Sep;12(9):1575-83. PMID:15341723<ref>PMID:15341723</ref>
==See Also==
 
*[[Phytase 3D structures|Phytase 3D structures]]
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>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 3-phytase]]
[[Category: Aspergillus fumigatus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Hao, Q]]
[[Category: Hao Q]]
[[Category: Huang, Q]]
[[Category: Huang Q]]
[[Category: Lei, X G]]
[[Category: Lei XG]]
[[Category: Liu, Q]]
[[Category: Liu Q]]
[[Category: Big alpha/beta domain]]
[[Category: Catalytic dynamic]]
[[Category: Catalytic site]]
[[Category: Hydrolase]]
[[Category: Product release pathway]]
[[Category: Small alpha domain]]
[[Category: Water structure]]

Revision as of 11:32, 1 May 2024

Crystallographic snapshots of Aspergillus fumigatus phytase revealing its enzymatic dynamicsCrystallographic snapshots of Aspergillus fumigatus phytase revealing its enzymatic dynamics

Structural highlights

1skb is a 1 chain structure with sequence from Aspergillus fumigatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.58Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHYA_ASPFU Catalyzes the hydrolysis of inorganic orthophosphate from phytate.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1skb, resolution 1.58Å

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OCA
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