1b14: Difference between revisions

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-[[Image:1b14.gif|left|200px]]<br /><applet load="1b14" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1b14, resolution 2.4&Aring;" />
-'''ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS BINARY COMPLEX WITH NAD+'''<br />
-==Overview==
+==Alcohol Dehydrogenase from Drosophila Lebanonensis Binary Complex with NAD+==
-Drosophila alcohol dehydrogenase (DADH; EC 1.1.1.1) is a NAD(H)-dependent, oxidoreductase belonging to the short-chain dehydrogenases/reductases, (SDR) family. This homodimeric enzyme catalyzes the dehydrogenation of, alcohols to their respective ketones or aldehydes in the fruit-fly, Drosophila, both for metabolic assimilation and detoxification purposes., The crystal structure of the apo form of DADH, one of the first, biochemically characterized member of the SDR family, was solved at 1.9 A, resolution by Patterson methods. The initial model was improved by, crystallographic refinement accompanied by electron density averaging, R-factor=20.5%, R-free=23.8%.DADH subunits show an alpha/beta single, domain structure with a characteristic NAD(H) binding motif (Rossmann, fold). The peptide chain of a subunit is folded into a central, eight-stranded beta-sheet flanked on each side by three alpha-helices. The, dimers have local 2-fold symmetry. Dimer association is dominated by a, four-helix bundle motif as well as two C-terminal loops from each subunit, which represent a unique structural feature in SDR enzymes with known, structure.Three structural features are characteristic for the active site, architecture. (1) A deep cavity which is covered by a flexible loop (33, residues) and the C-terminal tail (11 residues) from the neighboring, subunit. The hydrophobic surface of the cavity is likely to increase the, specificity of this enzyme towards secondary aliphatic alcohols. (2) The, residues of the catalytic triad (Ser138, Tyr151, Lys155) are known to be, involved in enzymatic catalysis in the first line. The Tyr151 OH group is, involved in an ionic bond with the Lys155 side-chain. Preliminary, electrostatic calculations have provided evidence that the active form of, Tyr151 is a tyrosinate ion at physiological pH. (3) Three well-ordered, water molecules in hydrogen bond distance to side-chains of the catalytic, triad may be significant for the proton release steps in DADH catalysis.A, ternary structure-based sequence alignment with ten members of the SDR, family with known three-dimensional structure has suggested to define a, model consisting of four groups of residues, which relates the observed, low degree of sequence identity to quite similar folding patterns and, nearly identical distributions of residues involved in catalysis.
+<StructureSection load='1b14' size='340' side='right'caption='[[1b14]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1b14]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Scaptodrosophila_lebanonensis Scaptodrosophila lebanonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B14 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B14 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]] 2.4&#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></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=1b14 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b14 OCA], [https://pdbe.org/1b14 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b14 RCSB], [https://www.ebi.ac.uk/pdbsum/1b14 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b14 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADH_DROLE ADH_DROLE]
+== 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/b1/1b14_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=1b14 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Drosophila alcohol dehydrogenase (DADH) is an NAD+-dependent enzyme that catalyzes the oxidation of alcohols to aldehydes/ketones. DADH is the member of the short-chain dehydrogenases/reductases family (SDR) for which the largest amount of biochemical data has been gathered during the last three decades. The crystal structures of one binary form (NAD+) and three ternary complexes with NAD+.acetone, NAD+.3-pentanone and NAD+.cyclohexanone were solved at 2.4, 2.2, 1. 4 and 1.6 A resolution, respectively. From the molecular interactions observed, the reaction mechanism could be inferred. The structure of DADH undergoes a conformational change in order to bind the coenzyme. Furthermore, upon binding of the ketone, a region that was disordered in the apo form (186-191) gets stabilized and closes the active site cavity by creating either a small helix (NAD+. acetone, NAD+.3-pentanone) or an ordered loop (NAD+.cyclohexanone). The active site pocket comprises a hydrophobic bifurcated cavity which explains why the enzyme is more efficient in oxidizing secondary aliphatic alcohols (preferably R form) than primary ones. Difference Fourier maps showed that the ketone inhibitor molecule has undergone a covalent reaction with the coenzyme in all three ternary complexes. Due to the presence of the positively charged ring of the coenzyme (NAD+) and the residue Lys155, the amino acid Tyr151 is in its deprotonated (tyrosinate) state at physiological pH. Tyr151 can subtract a proton from the enolic form of the ketone and catalyze a nucleophilic attack of the Calphaatom to the C4 position of the coenzyme creating an NAD-ketone adduct. The binding of these NAD-ketone adducts to DADH accounts for the inactivation of the enzyme. The catalytic reaction proceeds in a similar way, involving the same amino acids as in the formation of the NAD-ketone adduct. The p Kavalue of 9-9.5 obtained by kinetic measurements on apo DADH can be assigned to a protonated Tyr151 which is converted to an unprotonated tyrosinate (p Ka7.6) by the influence of the positively charged nicotinamide ring in the binary enzyme-NAD+form. pH independence during the release of NADH from the binary complex enzyme-NADH can be explained by either a lack of electrostatic interaction between the coenzyme and Tyr151 or an apparent p Kavalue for this residue higher than 10.0.
-==About this Structure==
+The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: observation of an enzyme-bound NAD-ketone adduct at 1.4 A resolution by X-ray crystallography.,Benach J, Atrian S, Gonzalez-Duarte R, Ladenstein R J Mol Biol. 1999 Jun 4;289(2):335-55. PMID:10366509<ref>PMID:10366509</ref>
-B14 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Scaptodrosophila_lebanonensis Scaptodrosophila lebanonensis] with <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1] Known structural/functional Sites: <scene name='pdbsite=ACA:Catalytic+Triad'>ACA</scene>, <scene name='pdbsite=ACB:Catalytic+Triad'>ACB</scene>, <scene name='pdbsite=CAA:Ca2++Binding+Residues'>CAA</scene>, <scene name='pdbsite=CAB:Ca2++Binding+Residues'>CAB</scene>, <scene name='pdbsite=NA1:Nad+Binding+Motif+In+Dadhs+G(A)Xgxxg'>NA1</scene>, <scene name='pdbsite=NA2:Nad+Binding+Motif+In+Sdrs+Gxxxgxg'>NA2</scene>, <scene name='pdbsite=NA3:Nad/Nadp+Selectivity+Amino+Acid'>NA3</scene>, <scene name='pdbsite=NB1:Nad+Binding+Motif+In+Dadhs+G(A)Xgxxg'>NB1</scene>, <scene name='pdbsite=NB2:Nad+Binding+Motif+In+Sdrs+Gxxxgxg'>NB2</scene> and <scene name='pdbsite=NB3:Nad/Nadp+Selectivity+Amino+Acid'>NB3</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B14 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The refined crystal structure of Drosophila lebanonensis alcohol dehydrogenase at 1.9 A resolution., Benach J, Atrian S, Gonzalez-Duarte R, Ladenstein R, J Mol Biol. 1998 Sep 18;282(2):383-99. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9735295 9735295]
+</div>
-[[Category: Alcohol dehydrogenase]]
+<div class="pdbe-citations 1b14" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Scaptodrosophila lebanonensis]]
-[[Category: Single protein]]
+[[Category: Atrian S]]
-[[Category: Atrian, S.]]
+[[Category: Benach J]]
-[[Category: Benach, J.]]
+[[Category: Gonzalez-Duarte R]]
-[[Category: Gonzalez-Duarte, R.]]
+[[Category: Ladenstein R]]
-[[Category: Ladenstein, R.]]
-[[Category: NAD]]
-[[Category: alcohol dehydrogenase]]
-[[Category: binary complex]]
-[[Category: detoxification]]
-[[Category: drosophila lebanonensis]]
-[[Category: metabolism]]
-[[Category: short-chain dehydrogenases/reductases]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 09:32:19 2008''