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| | ==X-ray structure of cytoplasmic glyceraldehyde-3-phosphate dehydrogenase (GapC1) complexed with NAD== | | ==X-ray structure of cytoplasmic glyceraldehyde-3-phosphate dehydrogenase (GapC1) complexed with NAD== |
| - | <StructureSection load='4z0h' size='340' side='right' caption='[[4z0h]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='4z0h' size='340' side='right'caption='[[4z0h]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4z0h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z0H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4z0h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z0H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3k2b|3k2b]]</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </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=4z0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z0h OCA], [https://pdbe.org/4z0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z0h RCSB], [https://www.ebi.ac.uk/pdbsum/4z0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z0h 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=4z0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z0h OCA], [http://pdbe.org/4z0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z0h RCSB], [http://www.ebi.ac.uk/pdbsum/4z0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z0h ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/G3PC1_ARATH G3PC1_ARATH]] 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. Involved in response to oxidative stress by mediating plant responses to abscisic acid (ABA) and water deficits through the activation of PLDDELTA and production of phosphatidic acid (PA), a multifunctional stress signaling lipid in plants. Required for full fertility. Binds DNA in vitro.<ref>PMID:18820081</ref> <ref>PMID:22589465</ref> | + | [https://www.uniprot.org/uniprot/G3PC1_ARATH G3PC1_ARATH] 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. Involved in response to oxidative stress by mediating plant responses to abscisic acid (ABA) and water deficits through the activation of PLDDELTA and production of phosphatidic acid (PA), a multifunctional stress signaling lipid in plants. Required for full fertility. Binds DNA in vitro.<ref>PMID:18820081</ref> <ref>PMID:22589465</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4z0h" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4z0h" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Falini, G]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Fermani, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Orru, R]] | + | [[Category: Falini G]] |
| - | [[Category: Trost, P]] | + | [[Category: Fermani S]] |
| - | [[Category: Zaffagnini, M]] | + | [[Category: Orru R]] |
| - | [[Category: Cytoplasm]] | + | [[Category: Trost P]] |
| - | [[Category: Glycolysis]] | + | [[Category: Zaffagnini M]] |
| - | [[Category: Nad complex]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| Structural highlights
Function
G3PC1_ARATH 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. Involved in response to oxidative stress by mediating plant responses to abscisic acid (ABA) and water deficits through the activation of PLDDELTA and production of phosphatidic acid (PA), a multifunctional stress signaling lipid in plants. Required for full fertility. Binds DNA in vitro.[1] [2]
Publication Abstract from PubMed
AIMS: Cysteines and H2O2 are fundamental players in redox signaling. Cysteine thiol deprotonation favors the reaction with H2O2 that generates sulfenic acids with dual electrophilic/nucleophilic nature. The protein microenvironment surrounding the target cysteine is believed to control whether sulfenic acid can be reversibly regulated by disulfide formation or irreversibly oxidized to sulfinates/sulfonates. In this study, we present experimental oxidation kinetics and a quantum mechanical/molecular mechanical (QM/MM) investigation to elucidate the reaction of H2O2 with glycolytic and photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana (cytoplasmic AtGAPC1 and chloroplastic AtGAPA, respectively). RESULTS: Although AtGAPC1 and AtGAPA have almost identical 3D structure and similar acidity of their catalytic Cys149, AtGAPC1 is more sensitive to H2O2 and prone to irreversible oxidation than AtGAPA. As a result, sulfenic acid is more stable in AtGAPA. INNOVATION: Based on crystallographic structures of AtGAPC1 and AtGAPA, the reaction potential energy surface for Cys149 oxidation by H2O2 was calculated by QM. In both enzymes, sulfenic acid formation was characterized by a lower energy barrier than sulfinate formation, and sulfonate formation was prevented by very high energy barriers. Activation energies for both oxidation steps were lower in AtGAPC1 than AtGAPA, supporting the higher propensity of AtGAPC1 toward irreversible oxidation. CONCLUSIONS: QM/MM calculations coupled to fingerprinting analyses revealed that two Arg of AtGAPA (substituted by Gly and Val in AtGAPC1), located at 8-15 A distance from Cys149, are the major factors responsible for sulfenic acid stability, underpinning the importance of long-distance polar interactions in tuning sulfenic acid stability in native protein microenvironments.
Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana.,Zaffagnini M, Fermani S, Calvaresi M, Orru R, Iommarini L, Sparla F, Falini G, Bottoni A, Trost P Antioxid Redox Signal. 2016 Mar 20;24(9):502-17. doi: 10.1089/ars.2015.6417. Epub, 2016 Feb 1. PMID:26650776[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Rius SP, Casati P, Iglesias AA, Gomez-Casati DF. Characterization of Arabidopsis lines deficient in GAPC-1, a cytosolic NAD-dependent glyceraldehyde-3-phosphate dehydrogenase. Plant Physiol. 2008 Nov;148(3):1655-67. doi: 10.1104/pp.108.128769. Epub 2008 Sep, 26. PMID:18820081 doi:http://dx.doi.org/10.1104/pp.108.128769
- ↑ Guo L, Devaiah SP, Narasimhan R, Pan X, Zhang Y, Zhang W, Wang X. Cytosolic glyceraldehyde-3-phosphate dehydrogenases interact with phospholipase Ddelta to transduce hydrogen peroxide signals in the Arabidopsis response to stress. Plant Cell. 2012 May;24(5):2200-12. doi: 10.1105/tpc.111.094946. Epub 2012 May, 15. PMID:22589465 doi:http://dx.doi.org/10.1105/tpc.111.094946
- ↑ Zaffagnini M, Fermani S, Calvaresi M, Orru R, Iommarini L, Sparla F, Falini G, Bottoni A, Trost P. Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana. Antioxid Redox Signal. 2016 Mar 20;24(9):502-17. doi: 10.1089/ars.2015.6417. Epub, 2016 Feb 1. PMID:26650776 doi:http://dx.doi.org/10.1089/ars.2015.6417
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