2cf5: Difference between revisions

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-[[Image:2cf5.jpg|left|200px]]<br /><applet load="2cf5" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2cf5, resolution 2.0&Aring;" />
-'''CRYSTAL STRUCTURES OF THE ARABIDOPSIS CINNAMYL ALCOHOL DEHYDROGENASES, ATCAD5'''<br />
-==Overview==
+==Crystal Structures of the Arabidopsis Cinnamyl Alcohol Dehydrogenases, AtCAD5==
-The cinnamyl alcohol dehydrogenase (CAD) multigene family in planta, encodes proteins catalyzing the reductions of various phenylpropenyl, aldehyde derivatives in a substrate versatile manner, and whose metabolic, products are the precursors of structural lignins, health-related lignans, and various other metabolites. In Arabidopsis thaliana, the two isoforms, AtCAD5 and AtCAD4, are the catalytically most active being viewed as, mainly involved in the formation of guaiacyl/syringyl lignins. In this, study, we determined the crystal structures of AtCAD5 in the apo-form and, as a binary complex with NADP+, respectively, and modeled that of AtCAD4., Both AtCAD5 and AtCAD4 are dimers with two zinc ions per subunit and, belong to the Zn-dependent medium chain dehydrogenase/reductase (MDR), superfamily, on the basis of their overall 2-domain structures and, distribution of secondary structural elements. The catalytic Zn2+ ions in, both enzymes are tetrahedrally coordinated, but differ from those in horse, liver alcohol dehydrogenase since the carboxyl side-chain of Glu70 is, ligated to Zn2+ instead of water. Using AtCAD5, site-directed mutagenesis, of Glu70 to alanine resulted in loss of catalytic activity, thereby, indicating that perturbation of the Zn2+ coordination was sufficient to, abolish catalytic activity. The substrate-binding pockets of both AtCAD5, and AtCAD4 were also examined, and found to be significantly different and, smaller compared to that of a putative aspen sinapyl alcohol dehydrogenase, (SAD) and a putative yeast CAD. While the physiological roles of the aspen, SAD and the yeast CAD are uncertain, they nevertheless have a high, similarity in the overall 3D structures to AtCAD5 and 4. With the bona, fide CAD's from various species, nine out of the twelve residues which, constitute the proposed substrate-binding pocket were, however, conserved., This is provisionally considered as indicative of a characteristic, fingerprint for the CAD family.
+<StructureSection load='2cf5' size='340' side='right'caption='[[2cf5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2cf5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CF5 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2cf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cf5 OCA], [https://pdbe.org/2cf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cf5 RCSB], [https://www.ebi.ac.uk/pdbsum/2cf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cf5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CADH5_ARATH CADH5_ARATH] Involved in lignin biosynthesis in the floral stem. Catalyzes the final step specific for the production of lignin monomers. Catalyzes the NADPH-dependent reduction of coniferaldehyde, 5-hydroxyconiferaldehyde, sinapaldehyde, 4-coumaraldehyde and caffeyl aldehyde to their respective alcohols.<ref>PMID:12805615</ref> <ref>PMID:14745009</ref> <ref>PMID:15937231</ref>
+== 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/cf/2cf5_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=2cf5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The cinnamyl alcohol dehydrogenase (CAD) multigene family in planta encodes proteins catalyzing the reductions of various phenylpropenyl aldehyde derivatives in a substrate versatile manner, and whose metabolic products are the precursors of structural lignins, health-related lignans, and various other metabolites. In Arabidopsis thaliana, the two isoforms, AtCAD5 and AtCAD4, are the catalytically most active being viewed as mainly involved in the formation of guaiacyl/syringyl lignins. In this study, we determined the crystal structures of AtCAD5 in the apo-form and as a binary complex with NADP+, respectively, and modeled that of AtCAD4. Both AtCAD5 and AtCAD4 are dimers with two zinc ions per subunit and belong to the Zn-dependent medium chain dehydrogenase/reductase (MDR) superfamily, on the basis of their overall 2-domain structures and distribution of secondary structural elements. The catalytic Zn2+ ions in both enzymes are tetrahedrally coordinated, but differ from those in horse liver alcohol dehydrogenase since the carboxyl side-chain of Glu70 is ligated to Zn2+ instead of water. Using AtCAD5, site-directed mutagenesis of Glu70 to alanine resulted in loss of catalytic activity, thereby indicating that perturbation of the Zn2+ coordination was sufficient to abolish catalytic activity. The substrate-binding pockets of both AtCAD5 and AtCAD4 were also examined, and found to be significantly different and smaller compared to that of a putative aspen sinapyl alcohol dehydrogenase (SAD) and a putative yeast CAD. While the physiological roles of the aspen SAD and the yeast CAD are uncertain, they nevertheless have a high similarity in the overall 3D structures to AtCAD5 and 4. With the bona fide CAD's from various species, nine out of the twelve residues which constitute the proposed substrate-binding pocket were, however, conserved. This is provisionally considered as indicative of a characteristic fingerprint for the CAD family.
-==About this Structure==
+Crystal structures and catalytic mechanism of the Arabidopsis cinnamyl alcohol dehydrogenases AtCAD5 and AtCAD4.,Youn B, Camacho R, Moinuddin SG, Lee C, Davin LB, Lewis NG, Kang C Org Biomol Chem. 2006 May 7;4(9):1687-97. Epub 2006 Apr 4. PMID:16633561<ref>PMID:16633561</ref>
-CF5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Cinnamyl-alcohol_dehydrogenase Cinnamyl-alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.195 1.1.1.195] Known structural/functional Site: <scene name='pdbsite=AC1:Zn+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CF5 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structures and catalytic mechanism of the Arabidopsis cinnamyl alcohol dehydrogenases AtCAD5 and AtCAD4., Youn B, Camacho R, Moinuddin SG, Lee C, Davin LB, Lewis NG, Kang C, Org Biomol Chem. 2006 May 7;4(9):1687-97. Epub 2006 Apr 4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16633561 16633561]
+</div>
+<div class="pdbe-citations 2cf5" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Acetylcholinesterase 3D structures|Acetylcholinesterase 3D structures]]
+*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Cinnamyl-alcohol dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Camacho R]]
-[[Category: Camacho, R.]]
+[[Category: Davin LB]]
-[[Category: Davin, L.]]
+[[Category: Kang C]]
-[[Category: Kang, C.]]
+[[Category: Lee C]]
-[[Category: Lee, C.]]
+[[Category: Lewis NG]]
-[[Category: Lewis, N.]]
+[[Category: Moinuddin S]]
-[[Category: Moinuddin, S.]]
+[[Category: Youn B]]
-[[Category: Youn, B.]]
-[[Category: ZN]]
-[[Category: lignin biosynthesis]]
-[[Category: metal-binding]]
-[[Category: nadp]]
-[[Category: oxidoreductase]]
-[[Category: zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb  3 10:34:33 2008''