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| | <StructureSection load='3v1y' size='340' side='right'caption='[[3v1y]], [[Resolution|resolution]] 1.86Å' scene=''> | | <StructureSection load='3v1y' size='340' side='right'caption='[[3v1y]], [[Resolution|resolution]] 1.86Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3v1y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V1Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3v1y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V1Y FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.86Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e5r|3e5r]], [[3e6a|3e6a]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GAPC, GPC, Os08g0126300, LOC_Os08g03290, OJ1163_G08.15, OsJ_024858 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </span></td></tr>
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| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3v1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1y OCA], [https://pdbe.org/3v1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v1y RCSB], [https://www.ebi.ac.uk/pdbsum/3v1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1y 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=3v1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v1y OCA], [https://pdbe.org/3v1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v1y RCSB], [https://www.ebi.ac.uk/pdbsum/3v1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v1y ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/G3PC1_ORYSJ G3PC1_ORYSJ]] Key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D-glyceroyl phosphate. Essential for the maintenance of cellular ATP levels and carbohydrate metabolism (By similarity).
| + | [https://www.uniprot.org/uniprot/G3PC1_ORYSJ G3PC1_ORYSJ] Key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D-glyceroyl phosphate. Essential for the maintenance of cellular ATP levels and carbohydrate metabolism (By similarity). |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | Cytosolic Oryza sativa glyceraldehyde-3-phosphate dehydrogenase (OsGAPDH), the enzyme involved in the ubiquitous glycolysis, catalyzes the oxidative phosphorylation of glyceraldehyde-3-phosphate to 1,3-biphosphoglycerate (BPG) using nicotinamide adenine dinucleotide (NAD) as an electron acceptor. We report crystal structures of OsGAPDH in three conditions of NAD-free, NAD-bound and sulfate-soaked forms to discuss the molecular determinants for coenzyme specificity. The structure of OsGAPDH showed a homotetramer form with each monomer comprising three domains-NAD-binding, catalytic and S-loop domains. NAD binds to each OsGAPDH subunits with some residues forming positively charged grooves that attract sulfate anions, as a simulation of phosphate groups in the product BPG. Phe37 not only forms a bottleneck to improve NAD-binding but also combines with Pro193 and Asp35 as key conserved residues for NAD-specificity in OsGAPDH. The binding of NAD alters the side-chain conformation of Phe37 with a 90 degrees rotation related to the adenine moiety of NAD, concomitant with clamping the active site about 0.6 A from the "open" to "closed" form, producing an increased affinity specific for NAD. Phe37 exists only in higher organisms, whereas it is replaced by other residues (Thr or Leu) with smaller side chains in lower organisms, which makes a greater distance between Leu34 and NAD of E. coli GAPDH than that between Phe37 and NAD of OsGAPDH. We demonstrated that Phe37 plays a crucial role in stabilizing NAD binding or intermediating of apo-holo transition, resulting in a greater NAD-dependent catalytic efficiency using site-directed mutagenesis. Phe37 might be introduced by evolution generating a catalytic advantage in cytosolic GAPDH.
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| - | Crystal structures of rice (Oryza sativa) glyceraldehyde-3-phosphate dehydrogenase complexes with NAD and sulfate suggest involvement of Phe37 in NAD binding for catalysis.,Tien YC, Chuankhayan P, Huang YC, Chen CD, Alikhajeh J, Chang SL, Chen CJ Plant Mol Biol. 2012 Nov;80(4-5):389-403. doi: 10.1007/s11103-012-9953-7. Epub, 2012 Aug 18. PMID:22903596<ref>PMID:22903596</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3v1y" style="background-color:#fffaf0;"></div>
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| | | | |
| | ==See Also== | | ==See Also== |
| | *[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]] | | *[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Japanese rice]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chang, S L]] | + | [[Category: Oryza sativa Japonica Group]] |
| - | [[Category: Chen, C J]] | + | [[Category: Chang SL]] |
| - | [[Category: Chuankhayan, P]] | + | [[Category: Chen CJ]] |
| - | [[Category: Lin, Y H]] | + | [[Category: Chuankhayan P]] |
| - | [[Category: Tien, Y C]] | + | [[Category: Lin YH]] |
| - | [[Category: Oxidoreductase]] | + | [[Category: Tien YC]] |
| - | [[Category: Rossmann fold]]
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