1nqa: Difference between revisions

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-{{Seed}}
-[[Image:1nqa.png|left|200px]]
-<!--
+==Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Replaced By Ala Complexed With Nad+ and D-Glyceraldehyde-3-Phosphate==
-The line below this paragraph, containing "STRUCTURE_1nqa", creates the "Structure Box" on the page.
+<StructureSection load='1nqa' size='340' side='right'caption='[[1nqa]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1nqa]] 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=1NQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NQA FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G3H:GLYCERALDEHYDE-3-PHOSPHATE'>G3H</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-{{STRUCTURE_1nqa|  PDB=1nqa  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nqa OCA], [https://pdbe.org/1nqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nqa RCSB], [https://www.ebi.ac.uk/pdbsum/1nqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nqa ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/G3P_GEOSE G3P_GEOSE]
+== 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/nq/1nqa_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=1nqa ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus stearothermophilus was solved in complex with its cofactor, NAD, and its physiological substrate, D-glyceraldehyde 3-phosphate (D-G3P). To isolate a stable ternary complex, the nucleophilic residue of the active site, Cys(149), was substituted with alanine or serine. The C149A and C149S GAPDH ternary complexes were obtained by soaking the crystals of the corresponding binary complexes (enzyme.NAD) in a solution containing G3P. The structures of the two binary and the two ternary complexes are presented. The D-G3P adopts the same conformation in the two ternary complexes. It is bound in a non-covalent way, in the free aldehyde form, its C-3 phosphate group being positioned in the P(s) site and not in the P(i) site. Its C-1 carbonyl oxygen points toward the essential His(176), which supports the role proposed for this residue along the two steps of the catalytic pathway. Arguments are provided that the structures reported here are representative of a productive enzyme.NAD.D-G3P complex in the ground state (Michaelis complex).
-===Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Replaced By Ala Complexed With Nad+ and D-Glyceraldehyde-3-Phosphate===
+Crystal structure of two ternary complexes of phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus with NAD and D-glyceraldehyde 3-phosphate.,Didierjean C, Corbier C, Fatih M, Favier F, Boschi-Muller S, Branlant G, Aubry A J Biol Chem. 2003 Apr 11;278(15):12968-76. Epub 2003 Feb 4. PMID:12569100<ref>PMID:12569100</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1nqa" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12569100}}, adds the Publication Abstract to the page
+*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12569100 is the PubMed ID number.
+*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_12569100}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-NQA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQA OCA].
-==Reference==
-Crystal structure of two ternary complexes of phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus with NAD and D-glyceraldehyde 3-phosphate., Didierjean C, Corbier C, Fatih M, Favier F, Boschi-Muller S, Branlant G, Aubry A, J Biol Chem. 2003 Apr 11;278(15):12968-76. Epub 2003 Feb 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12569100 12569100]
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Aubry, A.]]
+[[Category: Aubry A]]
-[[Category: Boschi-Muller, S.]]
+[[Category: Boschi-Muller S]]
-[[Category: Branlant, G.]]
+[[Category: Branlant G]]
-[[Category: Corbier, C.]]
+[[Category: Corbier C]]
-[[Category: Didierjean, C.]]
+[[Category: Didierjean C]]
-[[Category: Fatih, M.]]
+[[Category: Fatih M]]
-[[Category: Favier, F.]]
+[[Category: Favier F]]
-[[Category: Glycolysis]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 18:51:59 2008''