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5z3f

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Glycosidase E335A in complex with glucose

Structural highlights

5z3f is a 1 chain structure with sequence from Kribbella flavida DSM 17836. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.1Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IMGH_KRIFD Involved in the intracellular degradation of the cyclic tetrasaccharide cyclobis-(1-6)-alpha-nigerosyl (CNN) formed extracellularly from starch. Catalyzes the hydrolysis of alpha-1,6-glucosidic linkage from the non-reducing end of isomaltose to yield beta-D-glucose and D-glucose. Can also act on panose and isomaltotriose at a lower rate. It displays low or no activity toward CNN and the general GH15 enzyme substrates such as maltose, soluble starch or dextran.^[1]

Publication Abstract from PubMed

Glycoside hydrolase family 15 (GH15) inverting enzymes contain two glutamate residues functioning as a general acid catalyst and a general base catalyst, for isomaltose glucohydrolase (IGHase), Glu178 and Glu335, respectively. Generally, a two-catalytic residue-mediated reaction exhibits a typical bell-shaped pH-activity curve. However, IGHase is found to display atypical non-bell-shaped pH-kcat and pH-kcat /Km profiles, theoretically better-fitted to a three-catalytic residue-associated pH-activity curve. We determined the crystal structure of IGHase by the single-wavelength anomalous dispersion method using sulfur atoms and the cocrystal structure of a catalytic base mutant E335A with isomaltose. Although the activity of E335A was undetectable, the electron density observed in its active site pocket did not correspond to an isomaltose but a glycerol and a beta-glucose, cryoprotectant, and hydrolysis product. Our structural and biochemical analyses of several mutant enzymes suggest that Tyr48 acts as a second catalytic base catalyst. Y48F mutant displayed almost equivalent specific activity to a catalytic acid mutant E178A. Tyr48, highly conserved in all GH15 members, is fixed by another Tyr residue in many GH15 enzymes; the latter Tyr is replaced by Phe290 in IGHase. The pH profile of F290Y mutant changed to a bell-shaped curve, suggesting that Phe290 is a key residue distinguishing Tyr48 of IGHase from other GH15 members. Furthermore, F290Y is found to accelerate the condensation of isomaltose from glucose by modifying a hydrogen-bonding network between Tyr290-Tyr48-Glu335. The present study indicates that the atypical Phe290 makes Tyr48 of IGHase unique among GH15 enzymes.

Structural insights reveal the second base catalyst of isomaltose glucohydrolase.,Tagami T, Chen M, Furunaga Y, Kikuchi A, Sadahiro J, Lang W, Okuyama M, Tanaka Y, Iwasaki T, Yao M, Kimura A FEBS J. 2022 Feb;289(4):1118-1134. doi: 10.1111/febs.16237. Epub 2021 Oct 30. PMID:34665923^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tagami T, Miyano E, Sadahiro J, Okuyama M, Iwasaki T, Kimura A. Two Novel Glycoside Hydrolases Responsible for the Catabolism of Cyclobis-(1-->6)-alpha-nigerosyl. J Biol Chem. 2016 Aug 5;291(32):16438-47. doi: 10.1074/jbc.M116.727305. Epub 2016, Jun 14. PMID:27302067 doi:http://dx.doi.org/10.1074/jbc.M116.727305
↑ Tagami T, Chen M, Furunaga Y, Kikuchi A, Sadahiro J, Lang W, Okuyama M, Tanaka Y, Iwasaki T, Yao M, Kimura A. Structural insights reveal the second base catalyst of isomaltose glucohydrolase. FEBS J. 2022 Feb;289(4):1118-1134. doi: 10.1111/febs.16237. Epub 2021 Oct 30. PMID:34665923 doi:http://dx.doi.org/10.1111/febs.16237

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5z3f"

@@ Line 3: / Line 3: @@
 <StructureSection load='5z3f' size='340' side='right'caption='[[5z3f]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5z3f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Krifd Krifd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z3F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5z3f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Kribbella_flavida_DSM_17836 Kribbella flavida DSM 17836]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z3F FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.1&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Kfla_1896 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=479435 KRIFD])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5z3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3f OCA], [https://pdbe.org/5z3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z3f RCSB], [https://www.ebi.ac.uk/pdbsum/5z3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/IMGH_KRIFD IMGH_KRIFD]] Involved in the intracellular degradation of the cyclic tetrasaccharide cyclobis-(1-6)-alpha-nigerosyl (CNN) formed extracellularly from starch. Catalyzes the hydrolysis of alpha-1,6-glucosidic linkage from the non-reducing end of isomaltose to yield beta-D-glucose and D-glucose. Can also act on panose and isomaltotriose at a lower rate. It displays low or no activity toward CNN and the general GH15 enzyme substrates such as maltose, soluble starch or dextran.<ref>PMID:27302067</ref>
+[https://www.uniprot.org/uniprot/IMGH_KRIFD IMGH_KRIFD] Involved in the intracellular degradation of the cyclic tetrasaccharide cyclobis-(1-6)-alpha-nigerosyl (CNN) formed extracellularly from starch. Catalyzes the hydrolysis of alpha-1,6-glucosidic linkage from the non-reducing end of isomaltose to yield beta-D-glucose and D-glucose. Can also act on panose and isomaltotriose at a lower rate. It displays low or no activity toward CNN and the general GH15 enzyme substrates such as maltose, soluble starch or dextran.<ref>PMID:27302067</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Krifd]]
+[[Category: Kribbella flavida DSM 17836]]
 [[Category: Large Structures]]
-[[Category: Chen, M]]
+[[Category: Chen M]]
-[[Category: Kimura, A]]
+[[Category: Kimura A]]
-[[Category: Tagami, T]]
+[[Category: Tagami T]]
-[[Category: Tanaka, Y]]
+[[Category: Tanaka Y]]
-[[Category: Yao, M]]
+[[Category: Yao M]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]

5z3f

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Current revision

Glycosidase E335A in complex with glucose

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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