1kc1: Difference between revisions

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-[[Image:1kc1.jpg|left|200px]]<br /><applet load="1kc1" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1kc1, resolution 2.60&Aring;" />
-'''Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH'''<br />
-==Overview==
+==Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH==
-dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) catalyzes the final step in the conversion of dTDP-D-glucose to dTDP-L-rhamnose in an NAD(P)H- and Mg2+-dependent reaction. L-rhamnose biosynthesis is an antibacterial target. The structure of RmlD from Salmonella enterica serovar Typhimurium has been determined, and complexes with NADH, NADPH, and dTDP-L-rhamnose are reported. RmlD differs from other short chain dehydrogenases in that it has a novel dimer interface that contains Mg2+. Enzyme catalysis involves hydride transfer from the nicotinamide ring of the cofactor to the C4'-carbonyl group of the substrate. The substrate is activated through protonation by a conserved tyrosine. NAD(P)H is bound in a solvent-exposed cleft, allowing facile replacement. We suggest a novel role for the conserved serine/threonine residue of the catalytic triad of SDR enzymes.
+<StructureSection load='1kc1' size='340' side='right'caption='[[1kc1]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1kc1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KC1 FirstGlance]. <br>
-KC1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=NDP:'>NDP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC1 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc1 OCA], [https://pdbe.org/1kc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1kc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kc1 ProSAT]</span></td></tr>
-Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode., Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH, Structure. 2002 Jun;10(6):773-86. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12057193 12057193]
+</table>
-[[Category: Salmonella typhimurium]]
+== Function ==
-[[Category: Single protein]]
+[https://www.uniprot.org/uniprot/RMLD_SALTY RMLD_SALTY] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.
-[[Category: dTDP-4-dehydrorhamnose reductase]]
+== Evolutionary Conservation ==
-[[Category: Blankenfeldt, W.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Giraud, M F.]]
+Check<jmol>
-[[Category: Graninger, M.]]
+  <jmolCheckbox>
-[[Category: Kerr, I D.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kc/1kc1_consurf.spt"</scriptWhenChecked>
-[[Category: Leonard, G A.]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: McMiken, H J.]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: Messner, P.]]
+  </jmolCheckbox>
-[[Category: Naismith, J H.]]
+</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=1kc1 ConSurf].
-[[Category: Whitfield, C.]]
+<div style="clear:both"></div>
-[[Category: MG]]
+__TOC__
-[[Category: NDP]]
+</StructureSection>
-[[Category: SO4]]
+[[Category: Large Structures]]
-[[Category: rossman-fold]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: sugar-nucleotide-binding domain]]
+[[Category: Blankenfeldt W]]
+[[Category: Giraud MF]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:32:24 2008''
+[[Category: Graninger M]]
+[[Category: Kerr ID]]
+[[Category: Leonard GA]]
+[[Category: McMiken HJ]]
+[[Category: Messner P]]
+[[Category: Naismith JH]]
+[[Category: Whitfield C]]