|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='5axh' size='340' side='right'caption='[[5axh]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='5axh' size='340' side='right'caption='[[5axh]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5axh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermohydrosulfuricum Clostridium thermohydrosulfuricum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AXH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5axh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacter_pseudethanolicus_ATCC_33223 Thermoanaerobacter pseudethanolicus ATCC 33223]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AXH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AXH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5axg|5axg]]</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Teth39_0264 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=340099 Clostridium thermohydrosulfuricum])</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=5axh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axh OCA], [https://pdbe.org/5axh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5axh RCSB], [https://www.ebi.ac.uk/pdbsum/5axh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5axh ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5axh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5axh OCA], [http://pdbe.org/5axh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5axh RCSB], [http://www.ebi.ac.uk/pdbsum/5axh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5axh ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/B0KBZ7_THEP3 B0KBZ7_THEP3] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 23: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Clostridium thermohydrosulfuricum]] | |
| - | [[Category: Dextranase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Fujimoto, Z]] | + | [[Category: Thermoanaerobacter pseudethanolicus ATCC 33223]] |
| - | [[Category: Kim, Y M]] | + | [[Category: Fujimoto Z]] |
| - | [[Category: Kimura, A]] | + | [[Category: Kim YM]] |
| - | [[Category: Kishine, N]] | + | [[Category: Kimura A]] |
| - | [[Category: Ko, J A]] | + | [[Category: Kishine N]] |
| - | [[Category: Momma, M]] | + | [[Category: Ko JA]] |
| - | [[Category: Nam, S H]] | + | [[Category: Momma M]] |
| - | [[Category: Sakurai, M]] | + | [[Category: Nam SH]] |
| - | [[Category: Suzuki, N]] | + | [[Category: Sakurai M]] |
| - | [[Category: Glycoside hydrolase family 66]]
| + | [[Category: Suzuki N]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
B0KBZ7_THEP3
Publication Abstract from PubMed
The crystal structures of the wild type and catalytic mutant Asp-312-->Gly in complex with isomaltohexaose of endo-1,6-dextranase from the thermophilic bacterium Thermoanaerobacter pseudethanolicus (TpDex), belonging to the glycoside hydrolase family 66, were determined. TpDex consists of three structural domains, a catalytic domain comprising an (beta/alpha)8-barrel and two beta-domains located at both N- and C-terminal ends. The isomaltohexaose-complex structure demonstrated that the isomaltohexaose molecule was bound across the catalytic site, showing that TpDex had six subsites (-4 to +2) in the catalytic cleft. Marked movement of the Trp-376 side-chain along with loop 6, which was the side wall component of the cleft at subsite +1, was observed to occupy subsite +1, indicating that it might expel the cleaved aglycone subsite after the hydrolysis reaction. Structural comparison with other mesophilic enzymes indicated that several structural features of TpDex, loop deletion, salt bridge and surface-exposed charged residue, may contribute to thermostability.
Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus.,Suzuki N, Kishine N, Fujimoto Z, Sakurai M, Momma M, Ko JA, Nam SH, Kimura A, Kim YM J Biochem. 2016 Mar;159(3):331-9. doi: 10.1093/jb/mvv104. Epub 2015 Oct 21. PMID:26494689[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Suzuki N, Kishine N, Fujimoto Z, Sakurai M, Momma M, Ko JA, Nam SH, Kimura A, Kim YM. Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus. J Biochem. 2016 Mar;159(3):331-9. doi: 10.1093/jb/mvv104. Epub 2015 Oct 21. PMID:26494689 doi:http://dx.doi.org/10.1093/jb/mvv104
|
