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.
6vpb
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==A novel membrane-bound 6-phosphogluconate dehydrogenase from the acetic acid bacteria Gluconacetobacter diazotrophicus (Gd6PGD)== | ==A novel membrane-bound 6-phosphogluconate dehydrogenase from the acetic acid bacteria Gluconacetobacter diazotrophicus (Gd6PGD)== | ||
| - | <StructureSection load='6vpb' size='340' side='right'caption='[[6vpb]]' scene=''> | + | <StructureSection load='6vpb' size='340' side='right'caption='[[6vpb]], [[Resolution|resolution]] 1.87Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VPB OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[6vpb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gluda Gluda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VPB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VPB FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6vpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vpb OCA], [https://pdbe.org/6vpb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vpb RCSB], [https://www.ebi.ac.uk/pdbsum/6vpb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vpb ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The enzyme 6-phosphogluconate dehydrogenase catalyzes the conversion of 6-phosphogluconate to ribulose-5-phosphate. It represents an important reaction in the oxidative Pentose Phosphate Pathway, producing a ribose precursor essential for nucleotide and nucleic acid synthesis. We succeeded, for the first time, to determine the three-dimensional structure of this enzyme from an acetic acid bacterium, Gluconacetobacter diazotrophicus (Gd6PGD). Active Gd6PGD, a homodimer (70 kDa), was present both in the soluble and the membrane fraction of the nitrogen-fixing microorganism. The Gd6PGD belongs to the newly described subfamily of short-chain (333 AA) 6PGDs, compared to the long-chain subfamily (480 AA) (e.g. Ovis aries, Homo sapiens). The shorter amino acid sequence in Gd6PGD induces the exposition of hydrophobic residues in the C-terminal domain. This distinct structural feature is key for the protein to associate with the membrane. Furthermore, in terms of function, the short-chain 6PGD seems to prefer NAD(+) over NADP(+) , delivering NADH to the membrane-bound NADH dehydrogenase of the microorganisms required by the terminal oxidases to reduce dioxygen to water for energy conservation. | ||
| + | |||
| + | The structure of a novel membrane-associated 6-phosphogluconate dehydrogenase from Gluconacetobacter diazotrophicus (Gd6PGD) reveals a subfamily of short-chain 6PGDs.,Sarmiento-Pavia PD, Rodriguez-Hernandez A, Rodriguez-Romero A, Sosa-Torres ME FEBS J. 2020 Jul 4. doi: 10.1111/febs.15472. PMID:32621793<ref>PMID:32621793</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6vpb" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[6-phosphogluconate dehydrogenase 3D structures|6-phosphogluconate dehydrogenase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Gluda]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Rodriguez-Hernandez A]] | + | [[Category: Rodriguez-Hernandez, A]] |
| - | [[Category: Rodriguez-Romero A]] | + | [[Category: Rodriguez-Romero, A]] |
| + | [[Category: 6-phospho-d-gluconate]] | ||
| + | [[Category: 6-phosphogluconate dehydrogenase]] | ||
| + | [[Category: Gluconacetobacter diazotrophicus]] | ||
| + | [[Category: Membrane-bound protein]] | ||
| + | [[Category: Nad+]] | ||
| + | [[Category: Oxidoreductase]] | ||
Revision as of 17:50, 10 March 2021
A novel membrane-bound 6-phosphogluconate dehydrogenase from the acetic acid bacteria Gluconacetobacter diazotrophicus (Gd6PGD)
| |||||||||||
