1nyw: Difference between revisions

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-[[Image:1nyw.jpg|left|200px]]
- {{Structure
+==The high resolution structures of RmlC from Streptoccus suis in complex with dTDP-D-glucose==
-|PDB= 1nyw |SIZE=350|CAPTION= <scene name='initialview01'>1nyw</scene>, resolution 1.60&Aring;
+<StructureSection load='1nyw' size='340' side='right'caption='[[1nyw]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=DAU:2&#39;DEOXY-THYMIDINE-5&#39;-DIPHOSPHO-ALPHA-D-GLUCOSE'>DAU</scene>
+<table><tr><td colspan='2'>[[1nyw]] 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=1NYW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NYW FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_3,5-epimerase dTDP-4-dehydrorhamnose 3,5-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.13 5.1.3.13]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-|GENE= rmlc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1307 Streptococcus suis])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAU:2DEOXY-THYMIDINE-5-DIPHOSPHO-ALPHA-D-GLUCOSE'>DAU</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=1nyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nyw OCA], [https://pdbe.org/1nyw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nyw RCSB], [https://www.ebi.ac.uk/pdbsum/1nyw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nyw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8GIQ0_STRSU Q8GIQ0_STRSU]
+== 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/ny/1nyw_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=1nyw ConSurf].
+<div style="clear:both"></div>
-'''The high resolution structures of RmlC from Streptoccus suis in complex with dTDP-D-glucose'''
+==See Also==
+*[[RmlC|RmlC]]
+__TOC__
-==Overview==
+</StructureSection>
-Nature achieves the epimerization of carbohydrates by a variety of chemical routes. One common route is that performed by the class of enzyme defined by dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (RmlC) from the rhamnose pathway. Earlier studies failed to identify the key residues in catalysis. We report the 1.3 A structure of RmlC from Streptococcus suis type 2 and its complexes with dTDP-D-glucose and dTDP-D-xylose. The streptococcal RmlC enzymes belong to a separate subgroup, sharing only 25% identity with RmlC from other bacteria, yet the S. suis enzyme has similar kinetic properties and structure to other RmlC enzymes. Structure, sequence alignment, and mutational analysis have now allowed reliable identification of the catalytic residues and their roles.
+[[Category: Large Structures]]
-==About this Structure==
-NYW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NYW OCA].
-==Reference==
-High-resolution structures of RmlC from Streptococcus suis in complex with substrate analogs locate the active site of this class of enzyme., Dong C, Major LL, Allen A, Blankenfeldt W, Maskell D, Naismith JH, Structure. 2003 Jun;11(6):715-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12791259 12791259]
-[[Category: Single protein]]
 [[Category: Streptococcus suis]]
-[[Category: dTDP-4-dehydrorhamnose 3,5-epimerase]]
+[[Category: Allen A]]
-[[Category: Allen, A.]]
+[[Category: Blankenfeldt W]]
-[[Category: Blankenfeldt, W.]]
+[[Category: Dong C]]
-[[Category: Dong, C.]]
+[[Category: Major LL]]
-[[Category: Major, L L.]]
+[[Category: Maskell D]]
-[[Category: Maskell, D.]]
+[[Category: Naismith JH]]
-[[Category: Naismith, J H.]]
-[[Category: DAU]]
-[[Category: jelly roll-like structure; beta sheet]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 12:58:32 2008''