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| | ==Structure of a UDP-glucose dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum== | | ==Structure of a UDP-glucose dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum== |
| - | <StructureSection load='3vtf' size='340' side='right' caption='[[3vtf]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='3vtf' size='340' side='right'caption='[[3vtf]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3vtf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyril Pyril]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VTF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3vtf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_islandicum_DSM_4184 Pyrobaculum islandicum DSM 4184]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VTF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</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]] 2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pisl_1505 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=384616 PYRIL])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </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=3vtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtf OCA], [https://pdbe.org/3vtf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vtf RCSB], [https://www.ebi.ac.uk/pdbsum/3vtf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vtf 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=3vtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vtf OCA], [http://pdbe.org/3vtf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vtf RCSB], [http://www.ebi.ac.uk/pdbsum/3vtf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vtf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A1RUM9_PYRIL A1RUM9_PYRIL] |
| | <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: Pyril]] | + | [[Category: Large Structures]] |
| - | [[Category: UDP-glucose 6-dehydrogenase]] | + | [[Category: Pyrobaculum islandicum DSM 4184]] |
| - | [[Category: Ohshima, T]] | + | [[Category: Ohshima T]] |
| - | [[Category: Sakuraba, H]] | + | [[Category: Sakuraba H]] |
| - | [[Category: Yoneda, K]] | + | [[Category: Yoneda K]] |
| - | [[Category: Dehydrogenase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Two discrete alpha/beta domain]]
| + | |
| Structural highlights
Function
A1RUM9_PYRIL
Publication Abstract from PubMed
The crystal structure of an extremely thermostable UDP-glucose dehydrogenase (UDP-GDH) from the hyperthermophilic archaeon Pyrobaculum islandicum was determined at a resolution of 2.0 A. The overall fold was comprised of an N-terminal NAD(+) dinucleotide binding domain and a C-terminal UDP-sugar binding domain connected by a long alpha-helix, and the main-chain coordinates of the enzyme were similar to those of previously studied UDP-GDHs, including the enzymes from Burkholderia cepacia, Streptococcus pyogenes and Klebsiella pneumoniae. However, the sizes of several surface loops in P. islandicum UDP-GDH were much smaller than the corresponding loops in B. cepacia UDP-GDH but were comparable to those of the S. pyogenes and K. pneumoniae enzymes. Structural comparison revealed that the presence of extensive intersubunit hydrophobic interactions, as well as the formation of an intersubunit aromatic pair network, is likely to be the main factor contributing to the hyperthermostability of P. islandicum UDP-GDH.
Structure of a UDP-glucose dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum.,Sakuraba H, Kawai T, Yoneda K, Ohshima T Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Sep;68(Pt 9):1003-7. Epub , 2012 Aug 29. PMID:22949183[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sakuraba H, Kawai T, Yoneda K, Ohshima T. Structure of a UDP-glucose dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Sep;68(Pt 9):1003-7. Epub , 2012 Aug 29. PMID:22949183 doi:http://dx.doi.org/10.1107/S1744309112030667
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