8h1m: Difference between revisions
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==Crystal structure of glucose-2-epimerase mutant_D254A from Runella slithyformis Runsl_4512== | |||
<StructureSection load='8h1m' size='340' side='right'caption='[[8h1m]], [[Resolution|resolution]] 1.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8h1m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Runella_slithyformis Runella slithyformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8H1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8H1M FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=8h1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h1m OCA], [https://pdbe.org/8h1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h1m RCSB], [https://www.ebi.ac.uk/pdbsum/8h1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h1m ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A7U4E834_RUNSL A0A7U4E834_RUNSL] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Mannose 2-epimerase (ME), a member of the acylglucosamine 2-epimerase (AGE) superfamily that catalyzes epimerization of D-mannose and D-glucose, has recently been characterized to have potential for D-mannose production. However, the substrate-recognition and catalytic mechanism of ME remains unknown. In this study, structures of Runella slithyformis ME (RsME) and its D254A mutant [RsME(D254A)] were determined in their apo forms and as intermediate-analog complexes [RsME-D-glucitol and RsME(D254A)-D-glucitol]. RsME possesses the (alpha/alpha)(6)-barrel of the AGE superfamily members but has a unique pocket-covering long loop (loop(alpha7-alpha8)). The RsME-D-glucitol structure showed that loop(alpha7-alpha8) moves towards D-glucitol and closes the active pocket. Trp251 and Asp254 in loop(alpha7-alpha8) are only conserved in MEs and interact with D-glucitol. Kinetic analyses of the mutants confirmed the importance of these residues for RsME activity. Moreover, the structures of RsME(D254A) and RsME(D254A)-D-glucitol revealed that Asp254 is vital for binding the ligand in a correct conformation and for active-pocket closure. Docking calculations and structural comparison with other 2-epimerases show that the longer loop(alpha7-alpha8) in RsME causes steric hindrance upon binding to disaccharides. A detailed substrate-recognition and catalytic mechanism for monosaccharide-specific epimerization in RsME has been proposed. | |||
Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis.,Wang H, Sun X, Saburi W, Hashiguchi S, Yu J, Ose T, Mori H, Yao M Acta Crystallogr D Struct Biol. 2023 Jul 1;79(Pt 7):585-595. doi: , 10.1107/S205979832300390X. Epub 2023 Jun 14. PMID:37314406<ref>PMID:37314406</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 8h1m" style="background-color:#fffaf0;"></div> | ||
[[Category: Saburi | == References == | ||
[[Category: | <references/> | ||
[[Category: Wang | __TOC__ | ||
[[Category: Yu | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Runella slithyformis]] | |||
[[Category: Saburi W]] | |||
[[Category: Sun XM]] | |||
[[Category: Wang H]] | |||
[[Category: Yao M]] | |||
[[Category: Yu J]] | |||
Latest revision as of 10:25, 12 July 2023
Crystal structure of glucose-2-epimerase mutant_D254A from Runella slithyformis Runsl_4512Crystal structure of glucose-2-epimerase mutant_D254A from Runella slithyformis Runsl_4512
Structural highlights
FunctionPublication Abstract from PubMedMannose 2-epimerase (ME), a member of the acylglucosamine 2-epimerase (AGE) superfamily that catalyzes epimerization of D-mannose and D-glucose, has recently been characterized to have potential for D-mannose production. However, the substrate-recognition and catalytic mechanism of ME remains unknown. In this study, structures of Runella slithyformis ME (RsME) and its D254A mutant [RsME(D254A)] were determined in their apo forms and as intermediate-analog complexes [RsME-D-glucitol and RsME(D254A)-D-glucitol]. RsME possesses the (alpha/alpha)(6)-barrel of the AGE superfamily members but has a unique pocket-covering long loop (loop(alpha7-alpha8)). The RsME-D-glucitol structure showed that loop(alpha7-alpha8) moves towards D-glucitol and closes the active pocket. Trp251 and Asp254 in loop(alpha7-alpha8) are only conserved in MEs and interact with D-glucitol. Kinetic analyses of the mutants confirmed the importance of these residues for RsME activity. Moreover, the structures of RsME(D254A) and RsME(D254A)-D-glucitol revealed that Asp254 is vital for binding the ligand in a correct conformation and for active-pocket closure. Docking calculations and structural comparison with other 2-epimerases show that the longer loop(alpha7-alpha8) in RsME causes steric hindrance upon binding to disaccharides. A detailed substrate-recognition and catalytic mechanism for monosaccharide-specific epimerization in RsME has been proposed. Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis.,Wang H, Sun X, Saburi W, Hashiguchi S, Yu J, Ose T, Mori H, Yao M Acta Crystallogr D Struct Biol. 2023 Jul 1;79(Pt 7):585-595. doi: , 10.1107/S205979832300390X. Epub 2023 Jun 14. PMID:37314406[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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