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| [[Image:1dbv.gif|left|200px]]
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| {{Structure
| | ==GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH ASP 32 REPLACED BY GLY, LEU 187 REPLACED BY ALA, AND PRO 188 REPLACED BY SER COMPLEXED WITH NAD+== |
| |PDB= 1dbv |SIZE=350|CAPTION= <scene name='initialview01'>1dbv</scene>, resolution 2.5Å
| | <StructureSection load='1dbv' size='340' side='right'caption='[[1dbv]], [[Resolution|resolution]] 2.50Å' scene=''> |
| |SITE= | | == Structural highlights == |
| |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
| | <table><tr><td colspan='2'>[[1dbv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBV FirstGlance]. <br> |
| |ACTIVITY= [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]
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| |GENE= GAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus]) | | <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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbv OCA], [https://pdbe.org/1dbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbv RCSB], [https://www.ebi.ac.uk/pdbsum/1dbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbv ProSAT]</span></td></tr> |
| | </table> |
| | == Function == |
| | [https://www.uniprot.org/uniprot/G3P_GEOSE G3P_GEOSE] |
| | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> |
| | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/1dbv_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> |
| | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dbv ConSurf]. |
| | <div style="clear:both"></div> |
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| '''GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH ASP 32 REPLACED BY GLY, LEU 187 REPLACED BY ALA, AND PRO 188 REPLACED BY SER COMPLEXED WITH NAD+'''
| | ==See Also== |
| | | *[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]] |
| | | *[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]] |
| ==Overview== | | __TOC__ |
| Mutations have been introduced in the cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus stearothermophilus in order to convert its cofactor selectivity from a specificity towards NAD into a preference for NADP. In the B-S mutant, five mutations (L33T, T34G, D35G, L187A, P188S) were selected on the basis of a sequence alignment with NADP-dependent chloroplastic GAPDHs. In the D32G-S mutant, two of the five mutations mentioned above (L187A, P188S) have been used in combination with another one designed from electrostatic considerations (D32G). Both mutants exhibit a dual-cofactor selectivity at the advantage of either NAD (B-S) or NADP (D32G-S). In order to analyse the cofactor-binding site plasticity at the molecular level, crystal structures of these mutants have been solved, when complexed with either NAD+ (D32G-Sn, resolution 2.5 A, R = 13.9%; B-Sn, 2.45 A, 19.3%) or NADP+ (D32G-Sp, 2.2 A, 19.2%; B-Sp, 2.5 A, 14.4%). The four refined models are very similar to that of the wild-type GAPDH and as expected resemble more closely the holo form than the apo form. In the B-S mutant, the wild-type low affinity for NADP+ seems to be essentially retained because of repulsive electrostatic contacts between the extra 2'-phosphate and the unchanged carboxylate group of residue D32. Such an antideterminant effect is not well compensated by putative attractive interactions which had been expected to arise from the newly-introduced side-chains. In this mutant, recognition of NAD+ is slightly affected with respect to that known on the wild-type, because mutations only weakly destabilize hydrogen bonds and van der Waals contacts originally present in the natural enzyme. Thus, the B-S mutant does not mimic efficiently the chloroplastic GAPDHs, and long-range and/or second-layer effects, not easily predictable from visual inspection of three-dimensional structures, need to be taken into account for designing a true "chloroplastic-like" mutant of cytosolic GAPDH. In the case of the D32G-S mutant, the dissociation constants for NAD+ and NADP+ are practically reversed with respect to those of the wild-type. The strong alteration of the affinity for NAD+ obviously proceeds from the suppression of the two wild-type hydrogen bonds between the adenosine 2'- and 3'-hydroxyl positions and the D32 carboxylate group. As expected, the efficient recognition of NADP+ is partly promoted by the removal of intra-subunit electrostatic repulsion (D32G) and inter-subunit steric hindrance (L187A, P188S). Another interesting feature of the reshaped NADP+-binding site is provided by the local stabilization of the extra 2'-phosphate which forms a hydrogen bond with the side-chain hydroxyl group of the newly-introduced S188. When compared to the presently known natural NADP-binding clefts, this result clearly demonstrates that an absolute need for a salt-bridge involving the 2'-phosphate is not required to switch the cofactor selectivity from NAD to NADP. In fact, as it is the case in this mutant, only a moderately polar hydrogen bond can be sufficient to make the extra 2'-phosphate of NADP+ well recognized by a protein environment.
| | </StructureSection> |
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| ==About this Structure==
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| 1DBV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBV OCA].
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| ==Reference==
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| A crystallographic comparison between mutated glyceraldehyde-3-phosphate dehydrogenases from Bacillus stearothermophilus complexed with either NAD+ or NADP+., Didierjean C, Rahuel-Clermont S, Vitoux B, Dideberg O, Branlant G, Aubry A, J Mol Biol. 1997 May 16;268(4):739-59. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9175858 9175858]
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| [[Category: Geobacillus stearothermophilus]] | | [[Category: Geobacillus stearothermophilus]] |
| [[Category: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)]] | | [[Category: Large Structures]] |
| [[Category: Single protein]]
| | [[Category: Aubry A]] |
| [[Category: Aubry, A.]] | | [[Category: Branlant G]] |
| [[Category: Branlant, G.]] | | [[Category: Dideberg O]] |
| [[Category: Dideberg, O.]] | | [[Category: Didierjean C]] |
| [[Category: Didierjean, C.]] | | [[Category: Rahuel-Clermont S]] |
| [[Category: Rahuel-Clermont, S.]] | | [[Category: Vitoux B]] |
| [[Category: Vitoux, B.]] | |
| [[Category: NAD]]
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| [[Category: SO4]]
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| [[Category: nad(p) selectivity]]
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| [[Category: oxidoreductase]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:35:57 2008''
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