3dbv

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(New page: 200px<br /><applet load="3dbv" size="450" color="white" frame="true" align="right" spinBox="true" caption="3dbv, resolution 2.45&Aring;" /> '''GLYCERALDEHYDE-3-PHO...)
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[[Image:3dbv.jpg|left|200px]]<br /><applet load="3dbv" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="3dbv, resolution 2.45&Aring;" />
 
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'''GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH LEU 33 REPLACED BY THR, THR 34 REPLACED BY GLY, ASP 36 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 LEU 33 REPLACED BY THR, THR 34 REPLACED BY GLY, ASP 36 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='3dbv' size='340' side='right'caption='[[3dbv]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3dbv]] 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=3DBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DBV 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]] 2.45&#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=3dbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dbv OCA], [https://pdbe.org/3dbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dbv RCSB], [https://www.ebi.ac.uk/pdbsum/3dbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dbv 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/3dbv_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=3dbv 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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3DBV 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=3DBV 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 19:38:58 2007''
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Current revision

GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH LEU 33 REPLACED BY THR, THR 34 REPLACED BY GLY, ASP 36 REPLACED BY GLY, LEU 187 REPLACED BY ALA, AND PRO 188 REPLACED BY SER COMPLEXED WITH NAD+

PDB ID 3dbv

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