1dss

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[[Image:1dss.gif|left|200px]]<br /><applet load="1dss" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dss, resolution 1.88&Aring;" />
 
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'''STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR'''<br />
 
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==Overview==
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==STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR==
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The structure of active site carboxymethylated, D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor was, determined in the presence of coenzyme NAD+ at 1.88 A resolution with a, final R-factor of 0.175. The structure refinement was carried out on the, basis of the structure of holo-GAPDH at 2.0 A resolution using the program, XPLOR. The carboxymethyl group connected to Cys149 is stabilized by a, hydrogen bond between its OZ1 and Cys149N, and charge interaction between, the carboxyl group and the nicotinamide moiety. The modification of Cys149, induced conformational changes in the active site, in particular, the site, of sulphate ion 501 (the proposed attacking inorganic phosphate ion in, catalysis), and segment 208-218 nearby. Extensive hydrogen-bonding, interactions occur in the active site, which contribute to the higher, stability of the modified enzyme. The modification of the active site did, not affect the conformation of GAPDH elsewhere, including the subunit, interfaces. The structures of the green and red subunits in the asymmetric, unit are nearly identical, suggesting that the half-site reactivity of, this enzyme is from ligand-induced rather than pre-existing asymmetry. It, is proposed that the carboxymethyl group takes the place of the acyl group, of the reaction intermediate, and the catalytic mechanism of this enzyme, is discussed in the light of a comparison of the structures of the native, and the carboxymethylated GAPDH.
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<StructureSection load='1dss' size='340' side='right'caption='[[1dss]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1dss]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Panulirus_versicolor Panulirus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DSS 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]] 1.88&#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=CCS:CARBOXYMETHYLATED+CYSTEINE'>CCS</scene>, <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=1dss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dss OCA], [https://pdbe.org/1dss PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dss RCSB], [https://www.ebi.ac.uk/pdbsum/1dss PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dss ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/G3P_PANVR G3P_PANVR]
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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/ds/1dss_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=1dss 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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1DSS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Palinurus_versicolor Palinurus versicolor] 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] Known structural/functional Sites: <scene name='pdbsite=AVG:Active Site'>AVG</scene> and <scene name='pdbsite=AVR:Active Site'>AVR</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DSS 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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Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor., Song SY, Xu YB, Lin ZJ, Tsou CL, J Mol Biol. 1999 Apr 9;287(4):719-25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10191140 10191140]
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</StructureSection>
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[[Category: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)]]
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[[Category: Large Structures]]
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[[Category: Palinurus versicolor]]
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[[Category: Panulirus versicolor]]
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[[Category: Single protein]]
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[[Category: Lin Z]]
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[[Category: Lin, Z.]]
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[[Category: Song S]]
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[[Category: Song, S.]]
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[[Category: NAD]]
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[[Category: SO4]]
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[[Category: 'the-half-of-sites' reaction]]
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[[Category: active-site carboxymethylation]]
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[[Category: crystal structure]]
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[[Category: d-glyceraldehyde-3-phosphate-dehydrogenase]]
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[[Category: molecular symmetry]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 14:45:00 2007''
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Current revision

STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR

PDB ID 1dss

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