1czf: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1czf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CZF FirstGlance]. <br>
<table><tr><td colspan='2'>[[1czf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CZF 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.68&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] </span></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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1czf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1czf OCA], [https://pdbe.org/1czf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1czf RCSB], [https://www.ebi.ac.uk/pdbsum/1czf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1czf 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=1czf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1czf OCA], [https://pdbe.org/1czf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1czf RCSB], [https://www.ebi.ac.uk/pdbsum/1czf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1czf ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PGLR2_ASPNG PGLR2_ASPNG]] Involved in maceration and soft-rotting of plant tissue. Hydrolyzes the 1,4-alpha glycosidic bonds of de-esterified pectate in the smooth region of the plant cell wall.  
[https://www.uniprot.org/uniprot/PGLR2_ASPNA PGLR2_ASPNA] Involved in maceration and soft-rotting of plant tissue. Hydrolyzes the 1,4-alpha glycosidic bonds of de-esterified pectate in the smooth region of the plant cell wall.
== 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=1czf 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=1czf ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Polygalacturonases specifically hydrolyze polygalacturonate, a major constituent of plant cell wall pectin. To understand the catalytic mechanism and substrate and product specificity of these enzymes, we have solved the x-ray structure of endopolygalacturonase II of Aspergillus niger and we have carried out site-directed mutagenesis studies. The enzyme folds into a right-handed parallel beta-helix with 10 complete turns. The beta-helix is composed of four parallel beta-sheets, and has one very small alpha-helix near the N terminus, which shields the enzyme's hydrophobic core. Loop regions form a cleft on the exterior of the beta-helix. Site-directed mutagenesis of Asp(180), Asp(201), Asp(202), His(223), Arg(256), and Lys(258), which are located in this cleft, results in a severe reduction of activity, demonstrating that these residues are important for substrate binding and/or catalysis. The juxtaposition of the catalytic residues differs from that normally encountered in inverting glycosyl hydrolases. A comparison of the endopolygalacturonase II active site with that of the P22 tailspike rhamnosidase suggests that Asp(180) and Asp(202) activate the attacking nucleophilic water molecule, while Asp(201) protonates the glycosidic oxygen of the scissile bond.
1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis.,van Santen Y, Benen JA, Schroter KH, Kalk KH, Armand S, Visser J, Dijkstra BW J Biol Chem. 1999 Oct 22;274(43):30474-80. PMID:10521427<ref>PMID:10521427</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1czf" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Aspergillus niger]]
[[Category: Aspergillus niger]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Polygalacturonase]]
[[Category: Dijkstra BW]]
[[Category: Dijkstra, B W]]
[[Category: Kalk KH]]
[[Category: Kalk, K H]]
[[Category: Van Santen Y]]
[[Category: Santen, Y van]]
[[Category: Beta helix]]
[[Category: Hydrolase]]

Revision as of 18:44, 13 March 2024

ENDO-POLYGALACTURONASE II FROM ASPERGILLUS NIGERENDO-POLYGALACTURONASE II FROM ASPERGILLUS NIGER

Structural highlights

1czf is a 2 chain structure with sequence from Aspergillus niger. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.68Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PGLR2_ASPNA Involved in maceration and soft-rotting of plant tissue. Hydrolyzes the 1,4-alpha glycosidic bonds of de-esterified pectate in the smooth region of the plant cell wall.

Evolutionary Conservation

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

1czf, resolution 1.68Å

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OCA
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