1dc4: Difference between revisions

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-[[Image:1dc4.gif|left|200px]]
- {{Structure
+==STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES==
-|PDB= 1dc4 |SIZE=350|CAPTION= <scene name='initialview01'>1dc4</scene>, resolution 2.5&Aring;
+<StructureSection load='1dc4' size='340' side='right'caption='[[1dc4]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>
+<table><tr><td colspan='2'>[[1dc4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC4 FirstGlance]. <br>
-|ACTIVITY= [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]
+</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=G3P:SN-GLYCEROL-3-PHOSPHATE'>G3P</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1dc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc4 OCA], [https://pdbe.org/1dc4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc4 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/G3P1_ECOLI G3P1_ECOLI]
+== 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/dc/1dc4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1dc4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of gyceraldehyde 3-phosphate dehydrogenase (GAPDH) from Escherichia coli have been determined in three different enzymatic states, NAD(+)-free, NAD(+)-bound, and hemiacetal intermediate. The NAD(+)-free structure reported here has been determined from monoclinic and tetragonal crystal forms. The conformational changes in GAPDH induced by cofactor binding are limited to the residues that bind the adenine moiety of NAD(+). Glyceraldehyde 3-phosphate (GAP), the substrate of GAPDH, binds to the enzyme with its C3 phosphate in a hydrophilic pocket, called the "new P(i)" site, which is different from the originally proposed binding site for inorganic phosphate. This observed location of the C3 phosphate is consistent with the flip-flop model proposed for the enzyme mechanism [Skarzynski, T., Moody, P. C., and Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187]. Via incorporation of the new P(i) site in this model, it is now proposed that the C3 phosphate of GAP initially binds at the new P(i) site and then flips to the P(s) site before hydride transfer. A superposition of NAD(+)-bound and hemiacetal intermediate structures reveals an interaction between the hydroxyl oxygen at the hemiacetal C1 of GAP and the nicotinamide ring. This finding suggests that the cofactor NAD(+) may stabilize the transition state oxyanion of the hemiacetal intermediate in support of the flip-flop model for GAP binding.
-'''STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES'''
+Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes.,Yun M, Park CG, Kim JY, Park HW Biochemistry. 2000 Sep 5;39(35):10702-10. PMID:10978154<ref>PMID:10978154</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1dc4" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The crystal structures of gyceraldehyde 3-phosphate dehydrogenase (GAPDH) from Escherichia coli have been determined in three different enzymatic states, NAD(+)-free, NAD(+)-bound, and hemiacetal intermediate. The NAD(+)-free structure reported here has been determined from monoclinic and tetragonal crystal forms. The conformational changes in GAPDH induced by cofactor binding are limited to the residues that bind the adenine moiety of NAD(+). Glyceraldehyde 3-phosphate (GAP), the substrate of GAPDH, binds to the enzyme with its C3 phosphate in a hydrophilic pocket, called the "new P(i)" site, which is different from the originally proposed binding site for inorganic phosphate. This observed location of the C3 phosphate is consistent with the flip-flop model proposed for the enzyme mechanism [Skarzynski, T., Moody, P. C., and Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187]. Via incorporation of the new P(i) site in this model, it is now proposed that the C3 phosphate of GAP initially binds at the new P(i) site and then flips to the P(s) site before hydride transfer. A superposition of NAD(+)-bound and hemiacetal intermediate structures reveals an interaction between the hydroxyl oxygen at the hemiacetal C1 of GAP and the nicotinamide ring. This finding suggests that the cofactor NAD(+) may stabilize the transition state oxyanion of the hemiacetal intermediate in support of the flip-flop model for GAP binding.
+*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
+*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
-==About this Structure==
+== References ==
-DC4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC4 OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes., Yun M, Park CG, Kim JY, Park HW, Biochemistry. 2000 Sep 5;39(35):10702-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10978154 10978154]
 [[Category: Escherichia coli]]
-[[Category: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Kim J-Y]]
-[[Category: Kim, J Y.]]
+[[Category: Park C-G]]
-[[Category: Park, C G.]]
+[[Category: Park H-W]]
-[[Category: Park, H W.]]
+[[Category: Yun M]]
-[[Category: Yun, M.]]
-[[Category: G3P]]
-[[Category: gap]]
-[[Category: gapdh]]
-[[Category: structure]]
-[[Category: substrate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:36:09 2008''