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1kc1

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(New page: 200px<br /><applet load="1kc1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kc1, resolution 2.60&Aring;" /> '''Crystal structure of...)
Current revision (07:45, 7 February 2024) (edit) (undo)
 
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[[Image:1kc1.jpg|left|200px]]<br /><applet load="1kc1" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kc1, resolution 2.60&Aring;" />
 
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'''Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH'''<br />
 
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==Overview==
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==Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH==
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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.
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<StructureSection load='1kc1' size='340' side='right'caption='[[1kc1]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<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>
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1KC1 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 MG, SO4 and NDP 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KC1 OCA].
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</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>
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<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>
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==Reference==
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<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>
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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]
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</table>
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[[Category: Salmonella typhimurium]]
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== Function ==
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[[Category: Single protein]]
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[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.
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[[Category: dTDP-4-dehydrorhamnose reductase]]
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== Evolutionary Conservation ==
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[[Category: Blankenfeldt, W.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Giraud, M.F.]]
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Check<jmol>
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[[Category: Graninger, M.]]
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<jmolCheckbox>
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[[Category: Kerr, I.D.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kc/1kc1_consurf.spt"</scriptWhenChecked>
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[[Category: Leonard, G.A.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: McMiken, H.J.]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: Messner, P.]]
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</jmolCheckbox>
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[[Category: Naismith, J.H.]]
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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=1kc1 ConSurf].
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[[Category: Whitfield, C.]]
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<div style="clear:both"></div>
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[[Category: MG]]
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__TOC__
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[[Category: NDP]]
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</StructureSection>
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[[Category: SO4]]
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[[Category: Large Structures]]
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[[Category: rossman-fold]]
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[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
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[[Category: sugar-nucleotide-binding domain]]
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[[Category: Blankenfeldt W]]
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[[Category: Giraud MF]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:02:37 2007''
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[[Category: Graninger M]]
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[[Category: Kerr ID]]
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[[Category: Leonard GA]]
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[[Category: McMiken HJ]]
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[[Category: Messner P]]
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[[Category: Naismith JH]]
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[[Category: Whitfield C]]

Current revision

Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH

PDB ID 1kc1

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