3wfa: Difference between revisions

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 ==Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase==
-<StructureSection load='3wfa' size='340' side='right' caption='[[3wfa]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='3wfa' size='340' side='right'caption='[[3wfa]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3wfa]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WFA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WFA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3wfa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WFA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDT:{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC+ACID'>EDT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2d73|2d73]], [[2zq0|2zq0]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDT:{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC+ACID'>EDT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<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=3wfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wfa OCA], [http://pdbe.org/3wfa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wfa RCSB], [http://www.ebi.ac.uk/pdbsum/3wfa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wfa 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=3wfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wfa OCA], [https://pdbe.org/3wfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wfa RCSB], [https://www.ebi.ac.uk/pdbsum/3wfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wfa ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SUSB_BACTN SUSB_BACTN]] Glucoamylase that hydrolyzes alpha-1,4-glucosidic linkages, alpha-1,6-, alpha-1,3- and alpha-1,2-glucosidic linkages during starch degradation.<ref>PMID:8955399</ref> <ref>PMID:18981178</ref>
+[https://www.uniprot.org/uniprot/SUSB_BACTN SUSB_BACTN] Glucoamylase that hydrolyzes alpha-1,4-glucosidic linkages, alpha-1,6-, alpha-1,3- and alpha-1,2-glucosidic linkages during starch degradation.<ref>PMID:8955399</ref> <ref>PMID:18981178</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The role of calcium ion in the active site of the inverting glycoside hydrolase family 97 enzyme, BtGH97a, was investigated through structural and kinetic studies. The calcium ion was likely directly involved in the catalytic reaction. The pH dependence of kcat/Km values in the presence or absence of calcium ion indicated that the calcium ion lowered the pKa of the base catalyst. The significant decreases in kcat/Km for hydrolysis of substrates with basic leaving groups in the absence of calcium ion confirmed that the calcium ion facilitated the leaving group departure.
+Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase.,Okuyama M, Yoshida T, Hondoh H, Mori H, Yao M, Kimura A FEBS Lett. 2014 Aug 25;588(17):3213-7. doi: 10.1016/j.febslet.2014.07.002. Epub , 2014 Jul 10. PMID:25017438<ref>PMID:25017438</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3wfa" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Alpha-glucosidase|Alpha-glucosidase]]
+*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hondoh, H]]
+[[Category: Bacteroides thetaiotaomicron]]
-[[Category: Kimura, A]]
+[[Category: Large Structures]]
-[[Category: Mori, H]]
+[[Category: Hondoh H]]
-[[Category: Okuyama, M]]
+[[Category: Kimura A]]
-[[Category: Yao, M]]
+[[Category: Mori H]]
-[[Category: Yoshida, T]]
+[[Category: Okuyama M]]
-[[Category: Calcium binding]]
+[[Category: Yao M]]
-[[Category: Hydrolase]]
+[[Category: Yoshida T]]
-[[Category: Inverting glycoside hydrolase]]
-[[Category: Tim barrel]]