2d4v: Difference between revisions

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 <StructureSection load='2d4v' size='340' side='right'caption='[[2d4v]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2d4v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"thiobacillus_crenatus"_emoto_1929 "thiobacillus crenatus" emoto 1929]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2d4v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidithiobacillus_thiooxidans Acidithiobacillus thiooxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4V FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=2d4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4v OCA], [https://pdbe.org/2d4v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4v RCSB], [https://www.ebi.ac.uk/pdbsum/2d4v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4v ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8GAX0_ACITH Q8GAX0_ACITH]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=2d4v ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of Acidithiobacillus thiooxidans isocitrate dehydrogenase complexed with NAD+ and citrate has been solved to a resolution of 1.9 A. The protein fold of this NAD+-dependent enzyme shares a high similarity with those of NADP+-dependent bacterial ICDHs. The NAD+ and the citrate are clearly identified in the active site cleft with a well-defined electron density. Asp-357 is the direct cofactor-specificity determinant that interacts with 2'-OH and 3'-OH of the adenosine ribose. The adenosine ribose takes a C2'-endo puckering conformation as previously reported for an NAD+-specific isopropylmalate dehydrogenase. The nicotinamide moiety of NAD+ has the amide NH2 group oriented in cis conformation with respect to the C4 carbon of the nicotinamide ring, slanted toward the bound citrate molecule with a dihedral angle of -21 degrees . The semi-empirical molecular orbital calculation suggests that the pro-R hydrogen atom at C4 of NADH would bear the largest negative charge when the amide NH2 group is in such conformation, suggesting that the amide group has a catalytically significant role in stabilizing the transition state as NADH is being formed during the hydride transfer catalysis.
-Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity.,Imada K, Tamura T, Takenaka R, Kobayashi I, Namba K, Inagaki K Proteins. 2008 Jan 1;70(1):63-71. PMID:17634983<ref>PMID:17634983</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2d4v" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Thiobacillus crenatus emoto 1929]]
+[[Category: Acidithiobacillus thiooxidans]]
 [[Category: Large Structures]]
-[[Category: Imada, K]]
+[[Category: Imada K]]
-[[Category: Inagaki, K]]
+[[Category: Inagaki K]]
-[[Category: Namba, K]]
+[[Category: Namba K]]
-[[Category: Tamura, T]]
+[[Category: Tamura T]]
-[[Category: Alpha and beta protein]]
-[[Category: Isocitrate/isopropylmalate dehydrogenase-like fold]]
-[[Category: Oxidoreductase]]