1npt: Difference between revisions

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-[[Image:1npt.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1npt", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1npt|  PDB=1npt  |  SCENE=  }}
-'''Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 replaced by Ala complexed with NAD+'''
+==Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 replaced by Ala complexed with NAD+==
+<StructureSection load='1npt' size='340' side='right'caption='[[1npt]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1npt]] 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=1NPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NPT 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]] 2.18&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=1npt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1npt OCA], [https://pdbe.org/1npt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1npt RCSB], [https://www.ebi.ac.uk/pdbsum/1npt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1npt 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/np/1npt_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=1npt 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).
-==Overview==
+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>
-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).
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-NPT 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=1NPT OCA].
+</div>
+<div class="pdbe-citations 1npt" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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]
+*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
+*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[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 Sat May  3 02:49:54 2008''