1eyy: Difference between revisions

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OCA

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-[[Image:1eyy.jpg|left|200px]]<br /><applet load="1eyy" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1eyy, resolution 2.5&Aring;" />
-'''CRYSTAL STRUCTURE OF THE NADP+ DEPENDENT ALDEHYDE DEHYDROGENASE FROM VIBRIO HARVEYI.'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF THE NADP+ DEPENDENT ALDEHYDE DEHYDROGENASE FROM VIBRIO HARVEYI.==
-Aldehyde dehydrogenase from the bioluminescent bacterium, Vibrio harveyi, catalyses the oxidation of long-chain aliphatic aldehydes to acids. The, enzyme is unique compared with other forms of aldehyde dehydrogenase in, that it exhibits a very high specificity and affinity for the cofactor, NADP(+). Structural studies of this enzyme and comparisons with other, forms of aldehyde dehydrogenase provide the basis for understanding the, molecular features that dictate these unique properties and will enhance, our understanding of the mechanism of catalysis for this class of enzyme., The X-ray structure of aldehyde dehydrogenase from V. harveyi has been, solved to 2.5-A resolution as a partial complex with the cofactor NADP(+), and to 2. 1-A resolution as a fully bound 'holo' complex. The cofactor, preference exhibited by different forms of the enzyme is predominantly, determined by the electrostatic environment surrounding the 2'-hydroxy or, the 2'-phosphate groups of the adenosine ribose moiety of NAD(+) or, NADP(+), respectively. In the NADP(+)-dependent structures the presence of, a threonine and a lysine contribute to the cofactor specificity. In the V., harveyi enzyme an arginine residue (Arg-210) contributes to the high, cofactor affinity through a pi stacking interaction with the adenine ring, system of the cofactor. Further differences between the V. harveyi enzyme, and other aldehyde dehydrogenases are seen in the active site, in, particular a histidine residue which is structurally conserved with, phosphorylating glyceraldehyde-3-phosphate dehydrogenase. This may suggest, an alternative mechanism for activation of the reactive cysteine residue, for nucleophilic attack.
+<StructureSection load='1eyy' size='340' side='right'caption='[[1eyy]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1eyy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_harveyi Vibrio harveyi]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cbz 1cbz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EYY 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]] 2.5&#8491;</td></tr>
+<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></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=1eyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eyy OCA], [https://pdbe.org/1eyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eyy RCSB], [https://www.ebi.ac.uk/pdbsum/1eyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eyy ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ALDH_VIBHA ALDH_VIBHA] Catalyzes the oxidation of long-chain aliphatic aldehydes to acids. May be implicated in controlling luminescence as it catalyzes the oxidation of the fatty aldehyde substrate for the light-emitting reaction.
+== 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/ey/1eyy_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=1eyy ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-EYY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_harveyi Vibrio harveyi] with NAP as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1CBZ. Active as [http://en.wikipedia.org/wiki/Aldehyde_dehydrogenase_(NAD(P)(+)) Aldehyde dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.5 1.2.1.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EYY OCA].
+*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structure of the NADP+-dependent aldehyde dehydrogenase from Vibrio harveyi: structural implications for cofactor specificity and affinity., Ahvazi B, Coulombe R, Delarge M, Vedadi M, Zhang L, Meighen E, Vrielink A, Biochem J. 2000 Aug 1;349 Pt 3:853-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10903148 10903148]
+[[Category: Large Structures]]
-[[Category: Aldehyde dehydrogenase (NAD(P)(+))]]
-[[Category: Single protein]]
 [[Category: Vibrio harveyi]]
-[[Category: Ahvazi, B.]]
+[[Category: Ahvazi B]]
-[[Category: Coulombe, R.]]
+[[Category: Coulombe R]]
-[[Category: Delarge, M.]]
+[[Category: Delarge M]]
-[[Category: Meighen, E.]]
+[[Category: Meighen E]]
-[[Category: Vedadi, M.]]
+[[Category: Vedadi M]]
-[[Category: Vrielink, A.]]
+[[Category: Vrielink A]]
-[[Category: Zhang, L.]]
+[[Category: Zhang L]]
-[[Category: NAP]]
-[[Category: nucleotide binding domain]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:26:58 2007''