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2gd1

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(New page: 200px<br /><applet load="2gd1" size="450" color="white" frame="true" align="right" spinBox="true" caption="2gd1, resolution 2.5&Aring;" /> '''COENZYME-INDUCED CONF...)
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[[Image:2gd1.jpg|left|200px]]<br /><applet load="2gd1" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2gd1, resolution 2.5&Aring;" />
 
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'''COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILLUS'''<br />
 
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==Overview==
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==COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILLUS==
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The structure of apo-glyceraldehyde-3-phosphate dehydrogenase (GAPDHase), from Bacillus stearothermophilus has been refined using a restrained, least-squares method. The final crystallographic R-factor is 0.177 for all, 53,315 reflections between 7.0 and 2.5 A. The resulting model has been, analysed with respect to lattice interactions, molecular symmetry, temperature factors and solvent structure showing that, apart from local, deviations due to intermolecular contact, the molecule exhibits a very, high degree of local 222 symmetry. Analysis of differences between the, structure of apo-GAPDHase and the previously refined holo-GAPDHase at 1.8, A resolution reveals details of conformational change in the enzyme, induced by cofactor binding. The change, which was previously described as, a rigid-body rotation of the coenzyme-binding domain with respect to the, catalytic domain, is of more complex nature and involves relative shifts, of several structural elements in the coenzyme-binding domain and some, small changes in the catalytic domain. A possible mechanism of this, conformational change is proposed based on the comparison of the refined, structures and model-building studies. According to this mechanism, the, adenosine moiety of NAD can initially bind to the protein in the, apo-enzyme conformation. Several attractive interactions resulting from, the initial binding of the coenzyme trigger conformational changes in the, molecule of GAPDHase that: (1) create the productive nicotinamide-moiety, binding site; (2) improve enzyme-coenzyme interactions at the adenosine, moiety; (3) modify the active site to optimize the positioning of, catalytic residues and ion-binding sites. Implications of the proposed, mechanism for existing experimental data on binding of NAD analogues to, GAPDHase are discussed.
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<StructureSection load='2gd1' size='340' side='right'caption='[[2gd1]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2gd1]] 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=2GD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GD1 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=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=2gd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gd1 OCA], [https://pdbe.org/2gd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gd1 RCSB], [https://www.ebi.ac.uk/pdbsum/2gd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gd1 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/gd/2gd1_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=2gd1 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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2GD1 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 as [http://en.wikipedia.org/wiki/ligand ligand]. 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=2GD1 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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Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus., Skarzynski T, Wonacott AJ, J Mol Biol. 1988 Oct 20;203(4):1097-118. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=3210237 3210237]
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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: Skarzynski T]]
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[[Category: Skarzynski, T.]]
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[[Category: Wonacott AJ]]
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[[Category: Wonacott, A.J.]]
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[[Category: SO4]]
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[[Category: oxidoreductase(aldehyde(d)-nad(a))]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:07:57 2007''
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Current revision

COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILLUS

PDB ID 2gd1

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