6vpb: Difference between revisions

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<StructureSection load='6vpb' size='340' side='right'caption='[[6vpb]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
<StructureSection load='6vpb' size='340' side='right'caption='[[6vpb]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<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>
<table><tr><td colspan='2'>[[6vpb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gluconacetobacter_diazotrophicus_PA1_5 Gluconacetobacter diazotrophicus PA1 5]. 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='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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.87&#8491;</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>
<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;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A9H324_GLUDA A9H324_GLUDA]
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6vpb" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[6-phosphogluconate dehydrogenase 3D structures|6-phosphogluconate dehydrogenase 3D structures]]
*[[6-phosphogluconate dehydrogenase 3D structures|6-phosphogluconate dehydrogenase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Gluda]]
[[Category: Gluconacetobacter diazotrophicus PA1 5]]
[[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]]

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