2d2i: Difference between revisions

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-[[Image:2d2i.gif|left|200px]]<br /><applet load="2d2i" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2d2i, resolution 2.50&Aring;" />
-'''Crystal Structure of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp. complexed with Nadp+'''<br />
-==Overview==
+==Crystal Structure of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp. complexed with Nadp+==
-The crystal structure of NADP-dependent glyceraldehyde-3-phosphate, dehydrogenase (NADP-GAPDH) from Synechococcus PCC 7942 (S. 7942) in, complex with NADP was solved by molecular replacement and refined to an R, factor of 19.1% and a free R factor of 24.0% at 2.5 A resolution. The, overall structure of NADP-GAPDH from S. 7942 was quite similar to those of, other bacterial and eukaryotic GAPDHs. The nicotinamide ring of NADP, which is involved in the redox reaction, was oriented toward the catalytic, site. The 2'-phosphate O atoms of NADP exhibited hydrogen bonds to the, hydroxyl groups of Ser194 belonging to the S-loop and Thr37. These, residues are therefore considered to be essential in the discrimination, between NADP and NAD molecules. The C-terminal region was estimated to, have an extremely flexible conformation and to play an important role in, the formation of the supramolecular complex phosphoribulokinase, (PRK)-regulatory peptide (CP12)-GAPDH, which regulates enzyme activities.
+<StructureSection load='2d2i' size='340' side='right'caption='[[2d2i]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2d2i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2I FirstGlance]. <br>
+</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>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=2d2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2i OCA], [https://pdbe.org/2d2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2i RCSB], [https://www.ebi.ac.uk/pdbsum/2d2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2i ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q55245_SYNSP Q55245_SYNSP]
+== 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/d2/2d2i_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=2d2i ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-D2I is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=NAP:'>NAP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(NADP(+))_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (NADP(+)) (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.13 1.2.1.13] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2I OCA].
+*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 complexed with NADP., Kitatani T, Nakamura Y, Wada K, Kinoshita T, Tamoi M, Shigeoka S, Tada T, Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006 Apr 1;62(Pt, 4):315-9. Epub 2006 Mar 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16582475 16582475]
+[[Category: Large Structures]]
-[[Category: Glyceraldehyde-3-phosphate dehydrogenase (NADP(+)) (phosphorylating)]]
+[[Category: Synechococcus sp]]
-[[Category: Single protein]]
+[[Category: Kinoshita T]]
-[[Category: Synechococcus sp.]]
+[[Category: Kitatani T]]
-[[Category: Kinoshita, T.]]
+[[Category: Nakamura Y]]
-[[Category: Kitatani, T.]]
+[[Category: Shigeoka S]]
-[[Category: Nakamura, Y.]]
+[[Category: Tada T]]
-[[Category: Shigeoka, S.]]
+[[Category: Tamoi M]]
-[[Category: Tada, T.]]
+[[Category: Wada K]]
-[[Category: Tamoi, M.]]
-[[Category: Wada, K.]]
-[[Category: NAP]]
-[[Category: SO4]]
-[[Category: glyceraldehyde 3-phosphate dehydrogenase]]
-[[Category: protein-nadp+ complex]]
-[[Category: rossmann fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:53:39 2008''