1dbv

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(New page: 200px<br /><applet load="1dbv" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dbv, resolution 2.5&Aring;" /> '''GLYCERALDEHYDE-3-PHOS...)
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[[Image:1dbv.gif|left|200px]]<br /><applet load="1dbv" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dbv, resolution 2.5&Aring;" />
 
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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+'''<br />
 
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==Overview==
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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+==
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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.
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<StructureSection load='1dbv' size='340' side='right'caption='[[1dbv]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<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>
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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=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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/G3P_GEOSE G3P_GEOSE]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/1dbv_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1DBV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with SO4 and NAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DBV OCA].
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*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
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*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
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==Reference==
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__TOC__
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=9175858 9175858]
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</StructureSection>
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
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[[Category: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Aubry A]]
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[[Category: Aubry, A.]]
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[[Category: Branlant G]]
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[[Category: Branlant, G.]]
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[[Category: Dideberg O]]
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[[Category: Dideberg, O.]]
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[[Category: Didierjean C]]
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[[Category: Didierjean, C.]]
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[[Category: Rahuel-Clermont S]]
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[[Category: Rahuel-Clermont, S.]]
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[[Category: Vitoux B]]
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[[Category: Vitoux, B.]]
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[[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://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:08:57 2007''
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Current revision

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 ID 1dbv

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