1ket: Difference between revisions

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OCA

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-[[Image:1ket.jpg|left|200px]]<br /><applet load="1ket" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ket, resolution 1.80&Aring;" />
-'''The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with thymidine diphosphate bound'''<br />
-==Overview==
+==The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with thymidine diphosphate bound==
-dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the, L-rhamnose biosynthetic pathway, where it catalyzes the conversion of, dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB, from Salmonella enterica serovar Typhimurium in complex with substrate, deoxythymidine 5'-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine, 5'-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in, complex with dTDP-D-glucose, dTDP, and deoxythymidine, 5'-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at, resolutions between 1.8 A and 2.4 A. The structures show that the active, sites are highly conserved. Importantly, the structures show that the, active site tyrosine functions directly as the active site base, and an, aspartic and glutamic acid pairing accomplishes the dehydration step of, the enzyme mechanism. We conclude that the substrate is required to move, within the active site to complete the catalytic cycle and that this, movement is driven by the elimination of water. The results provide, insight into members of the SDR superfamily.
+<StructureSection load='1ket' size='340' side='right'caption='[[1ket]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ket]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KET 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]] 1.8&#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>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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=1ket FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ket OCA], [https://pdbe.org/1ket PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ket RCSB], [https://www.ebi.ac.uk/pdbsum/1ket PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ket ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RMLB_STRMU RMLB_STRMU] Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction (By similarity).
+== 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/ke/1ket_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=1ket ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5'-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5'-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5'-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 A and 2.4 A. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily.
-==About this Structure==
+Toward a structural understanding of the dehydratase mechanism.,Allard ST, Beis K, Giraud MF, Hegeman AD, Gross JW, Wilmouth RC, Whitfield C, Graninger M, Messner P, Allen AG, Maskell DJ, Naismith JH Structure. 2002 Jan;10(1):81-92. PMID:11796113<ref>PMID:11796113</ref>
-KET is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis] with TYD and NAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KET OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Toward a structural understanding of the dehydratase mechanism., Allard ST, Beis K, Giraud MF, Hegeman AD, Gross JW, Wilmouth RC, Whitfield C, Graninger M, Messner P, Allen AG, Maskell DJ, Naismith JH, Structure. 2002 Jan;10(1):81-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11796113 11796113]
+</div>
-[[Category: Single protein]]
+<div class="pdbe-citations 1ket" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DTDP-glucose 4%2C6-dehydratase|DTDP-glucose 4%2C6-dehydratase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptococcus suis]]
-[[Category: dTDP-glucose 4,6-dehydratase]]
+[[Category: Allard STM]]
-[[Category: Allard, S.T.M.]]
+[[Category: Allen AG]]
-[[Category: Allen, A.G.]]
+[[Category: Beis K]]
-[[Category: Beis, K.]]
+[[Category: Giraud M-F]]
-[[Category: Giraud, M.F.]]
+[[Category: Graninger M]]
-[[Category: Graninger, M.]]
+[[Category: Gross JW]]
-[[Category: Gross, J.W.]]
+[[Category: Hegeman AD]]
-[[Category: Hegeman, A.D.]]
+[[Category: Messner P]]
-[[Category: Messner, P.]]
+[[Category: Naismith JH]]
-[[Category: Naismith, J.H.]]
+[[Category: Whitfield C]]
-[[Category: Whitfield, C.]]
-[[Category: NAD]]
-[[Category: TYD]]
-[[Category: rossmann fold]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:08:23 2007''