This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5agd

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

An inactive (D125N) variant of the catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with alpha-1,6-mannopentaose

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='5agd' size='340' side='right'caption='[[5agd]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5agd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_24 Atcc 24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AGD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5agd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AGD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 1.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d4a|4d4a]], [[4d4b|4d4b]], [[4d4c|4d4c]], [[4d4d|4d4d]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannan_endo-1,6-alpha-mannosidase Mannan endo-1,6-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.101 3.2.1.101] </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=5agd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5agd OCA], [https://pdbe.org/5agd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5agd RCSB], [https://www.ebi.ac.uk/pdbsum/5agd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5agd ProSAT]</span></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=5agd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5agd OCA], [http://pdbe.org/5agd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5agd RCSB], [http://www.ebi.ac.uk/pdbsum/5agd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5agd ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/Q9Z4P9_NIACI Q9Z4P9_NIACI]
-alpha-Mannosidases and alpha-mannanases have attracted attention for the insight they provide into nucleophilic substitution at the hindered anomeric center of alpha-mannosides, and the potential of mannosidase inhibitors as cellular probes and therapeutic agents. We report the conformational itinerary of the family GH76 alpha-mannanases studied through structural analysis of the Michaelis complex and synthesis and evaluation of novel aza/imino sugar inhibitors. A Michaelis complex in an O S2 conformation, coupled with distortion of an azasugar in an inhibitor complex to a high energy B2,5 conformation are rationalized through ab initio QM/MM metadynamics that show how the enzyme surface restricts the conformational landscape of the substrate, rendering the B2,5 conformation the most energetically stable on-enzyme. We conclude that GH76 enzymes perform catalysis using an itinerary that passes through O S2 and B2,5 not equal conformations, information that should inspire the development of new antifungal agents.
-Evidence for a Boat Conformation at the Transition State of GH76 alpha-1,6-Mannanases-Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism.,Thompson AJ, Speciale G, Iglesias-Fernandez J, Hakki Z, Belz T, Cartmell A, Spears RJ, Chandler E, Temple MJ, Stepper J, Gilbert HJ, Rovira C, Williams SJ, Davies GJ Angew Chem Int Ed Engl. 2015 Mar 13. doi: 10.1002/anie.201410502. PMID:25772148<ref>PMID:25772148</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5agd" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 24]]
 [[Category: Large Structures]]
-[[Category: Mannan endo-1,6-alpha-mannosidase]]
+[[Category: Niallia circulans]]
-[[Category: Belz, T]]
+[[Category: Belz T]]
-[[Category: Cartmell, A]]
+[[Category: Cartmell A]]
-[[Category: Chandler, E]]
+[[Category: Chandler E]]
-[[Category: Davies, G J]]
+[[Category: Davies GJ]]
-[[Category: Gilbert, H J]]
+[[Category: Gilbert HJ]]
-[[Category: Hakki, Z]]
+[[Category: Hakki Z]]
-[[Category: Iglesias-Fernandez, J]]
+[[Category: Iglesias-Fernandez J]]
-[[Category: Rovira, C]]
+[[Category: Rovira C]]
-[[Category: Spears, R J]]
+[[Category: Spears RJ]]
-[[Category: Speciale, G]]
+[[Category: Speciale G]]
-[[Category: Stepper, J]]
+[[Category: Stepper J]]
-[[Category: Temple, M J]]
+[[Category: Temple MJ]]
-[[Category: Thompson, A J]]
+[[Category: Thompson AJ]]
-[[Category: Williams, S J]]
+[[Category: Williams SJ]]
-[[Category: Alpha-mannanase]]
-[[Category: Cazy]]
-[[Category: Enzyme-carbohydrate interaction]]
-[[Category: Gh76]]
-[[Category: Glycosidase inhibition]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]
-[[Category: Mannan]]
-[[Category: Mannanase]]
-[[Category: Quantum mechanic]]
-[[Category: Transition state]]

5agd

From Proteopedia

Current revision

An inactive (D125N) variant of the catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with alpha-1,6-mannopentaose

Structural highlights

Function

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox