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| | ==Crystal structure of dextranase from Streptococcus mutans in complex with 4,5-epoxypentyl alpha-D-glucopyranoside== | | ==Crystal structure of dextranase from Streptococcus mutans in complex with 4,5-epoxypentyl alpha-D-glucopyranoside== |
| - | <StructureSection load='3vmp' size='340' side='right' caption='[[3vmp]], [[Resolution|resolution]] 1.88Å' scene=''> | + | <StructureSection load='3vmp' size='340' side='right'caption='[[3vmp]], [[Resolution|resolution]] 1.88Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3vmp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25175 Atcc 25175]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VMP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3vmp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VMP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=E5G:5-HYDROXYPENTYL+ALPHA-D-GLUCOPYRANOSIDE'>E5G</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.88Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vmn|3vmn]], [[3vmo|3vmo]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E5G:5-HYDROXYPENTYL+ALPHA-D-GLUCOPYRANOSIDE'>E5G</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dextranase Dextranase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.11 3.2.1.11] </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=3vmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vmp OCA], [https://pdbe.org/3vmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vmp RCSB], [https://www.ebi.ac.uk/pdbsum/3vmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vmp 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=3vmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vmp OCA], [http://pdbe.org/3vmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vmp RCSB], [http://www.ebi.ac.uk/pdbsum/3vmp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vmp ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DEXT_STRMU DEXT_STRMU] May play a role in sucrose-independent adherence to the pellicle-coated tooth surface. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 25175]] | + | [[Category: Large Structures]] |
| - | [[Category: Dextranase]] | + | [[Category: Streptococcus mutans]] |
| - | [[Category: Fujimoto, Z]] | + | [[Category: Fujimoto Z]] |
| - | [[Category: Funane, K]] | + | [[Category: Funane K]] |
| - | [[Category: Kim, Y M]] | + | [[Category: Kim YM]] |
| - | [[Category: Kimura, A]] | + | [[Category: Kimura A]] |
| - | [[Category: Momma, M]] | + | [[Category: Momma M]] |
| - | [[Category: Mori, H]] | + | [[Category: Mori H]] |
| - | [[Category: Okuyama, M]] | + | [[Category: Okuyama M]] |
| - | [[Category: Suzuki, N]] | + | [[Category: Suzuki N]] |
| - | [[Category: Glycoside hydrolase family 66]]
| + | |
| - | [[Category: Greek-key motif]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Immunoglobrin fold]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
DEXT_STRMU May play a role in sucrose-independent adherence to the pellicle-coated tooth surface.
Publication Abstract from PubMed
Dextranase is an enzyme that hydrolyzes dextran alpha-1,6 linkages. Streptococcus mutans dextranase belongs to glycoside hydrolase family 66, producing isomaltooligosaccharides of various sizes and consisting of at least five amino acid sequence regions. The crystal structure of the conserved fragment from Gln(100) to Ile(732) of S. mutans dextranase, devoid of its N- and C-terminal variable regions, was determined at 1.6 A resolution and found to contain three structural domains. Domain N possessed an immunoglobulin-like beta-sandwich fold; domain A contained the enzyme's catalytic module, comprising a (beta/alpha)(8)-barrel; and domain C formed a beta-sandwich structure containing two Greek key motifs. Two ligand complex structures were also determined, and, in the enzyme-isomaltotriose complex structure, the bound isomaltooligosaccharide with four glucose moieties was observed in the catalytic glycone cleft and considered to be the transglycosylation product of the enzyme, indicating the presence of four subsites, -4 to -1, in the catalytic cleft. The complexed structure with 4',5'-epoxypentyl-alpha-d-glucopyranoside, a suicide substrate of the enzyme, revealed that the epoxide ring reacted to form a covalent bond with the Asp(385) side chain. These structures collectively indicated that Asp(385) was the catalytic nucleophile and that Glu(453) was the acid/base of the double displacement mechanism, in which the enzyme showed a retaining catalytic character. This is the first structural report for the enzyme belonging to glycoside hydrolase family 66, elucidating the enzyme's catalytic machinery.
Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66.,Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K, Kimura A J Biol Chem. 2012 Jun 8;287(24):19916-26. doi: 10.1074/jbc.M112.342444. Epub 2012, Feb 15. PMID:22337884[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Suzuki N, Kim YM, Fujimoto Z, Momma M, Okuyama M, Mori H, Funane K, Kimura A. Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66. J Biol Chem. 2012 Jun 8;287(24):19916-26. doi: 10.1074/jbc.M112.342444. Epub 2012, Feb 15. PMID:22337884 doi:10.1074/jbc.M112.342444
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