2d2i: Difference between revisions

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-[[Image:2d2i.gif|left|200px]]
- {{Structure
+==Crystal Structure of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp. complexed with Nadp+==
-|PDB= 2d2i |SIZE=350|CAPTION= <scene name='initialview01'>2d2i</scene>, resolution 2.50&Aring;
+<StructureSection load='2d2i' size='340' side='right'caption='[[2d2i]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=NAP:NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE'>NAP</scene>
+<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>
-|ACTIVITY= [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]
+</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>
-|GENE=
+<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>
-'''Crystal Structure of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp. complexed with Nadp+'''
+==See Also==
+*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-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.
+[[Category: Large Structures]]
+[[Category: Synechococcus sp]]
-==About this Structure==
+[[Category: Kinoshita T]]
-D2I is a [[Single protein]] structure of sequence from [http://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].
+[[Category: Kitatani T]]
+[[Category: Nakamura Y]]
-==Reference==
+[[Category: Shigeoka S]]
-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 Crystallogr Sect F Struct Biol Cryst Commun. 2006 Apr 1;62(Pt, 4):315-9. Epub 2006 Mar 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16582475 16582475]
+[[Category: Tada T]]
-[[Category: Glyceraldehyde-3-phosphate dehydrogenase (NADP(+)) (phosphorylating)]]
+[[Category: Tamoi M]]
-[[Category: Single protein]]
+[[Category: Wada K]]
-[[Category: Synechococcus sp.]]
-[[Category: Kinoshita, T.]]
-[[Category: Kitatani, T.]]
-[[Category: Nakamura, Y.]]
-[[Category: Shigeoka, S.]]
-[[Category: Tada, T.]]
-[[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 Thu Mar 20 16:22:31 2008''