2ixl

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[[Image:2ixl.jpg|left|200px]]
 
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{{Structure
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==RmlC S. suis with dTDP-rhamnose==
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|PDB= 2ixl |SIZE=350|CAPTION= <scene name='initialview01'>2ixl</scene>, resolution 1.60&Aring;
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<StructureSection load='2ixl' size='340' side='right'caption='[[2ixl]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Trh+Binding+Site+For+Chain+D'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene> and <scene name='pdbligand=TRH:2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene>
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<table><tr><td colspan='2'>[[2ixl]] is a 4 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=2IXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IXL FirstGlance]. <br>
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|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]
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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]] 1.6&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene></td></tr>
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}}
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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=2ixl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ixl OCA], [https://pdbe.org/2ixl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ixl RCSB], [https://www.ebi.ac.uk/pdbsum/2ixl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ixl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q8GIQ0_STRSU Q8GIQ0_STRSU]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/2ixl_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2ixl ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The striking feature of carbohydrates is their constitutional, conformational and configurational diversity. Biology has harnessed this diversity and manipulates carbohydrate residues in a variety of ways, one of which is epimerization. RmlC catalyzes the epimerization of the C3' and C5' positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose. RmlC is the third enzyme of the rhamnose pathway, and represents a validated anti-bacterial drug target. Although several structures of the enzyme have been reported, the mechanism and the nature of the intermediates have remained obscure. Despite its relatively small size (22 kDa), RmlC catalyzes four stereospecific proton transfers and the substrate undergoes a major conformational change during the course of the transformation. Here we report the structure of RmlC from several organisms in complex with product and product mimics. We have probed site-directed mutants by assay and by deuterium exchange. The combination of structural and biochemical data has allowed us to assign key residues and identify the conformation of the carbohydrate during turnover. Clear knowledge of the chemical structure of RmlC reaction intermediates may offer new opportunities for rational drug design.
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'''RMLC S. SUIS WITH DTDP-RHAMNOSE'''
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RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation.,Dong C, Major LL, Srikannathasan V, Errey JC, Giraud MF, Lam JS, Graninger M, Messner P, McNeil MR, Field RA, Whitfield C, Naismith JH J Mol Biol. 2007 Jan 5;365(1):146-59. Epub 2006 Sep 29. PMID:17046787<ref>PMID:17046787</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2ixl" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The striking feature of carbohydrates is their constitutional, conformational and configurational diversity. Biology has harnessed this diversity and manipulates carbohydrate residues in a variety of ways, one of which is epimerization. RmlC catalyzes the epimerization of the C3' and C5' positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose. RmlC is the third enzyme of the rhamnose pathway, and represents a validated anti-bacterial drug target. Although several structures of the enzyme have been reported, the mechanism and the nature of the intermediates have remained obscure. Despite its relatively small size (22 kDa), RmlC catalyzes four stereospecific proton transfers and the substrate undergoes a major conformational change during the course of the transformation. Here we report the structure of RmlC from several organisms in complex with product and product mimics. We have probed site-directed mutants by assay and by deuterium exchange. The combination of structural and biochemical data has allowed us to assign key residues and identify the conformation of the carbohydrate during turnover. Clear knowledge of the chemical structure of RmlC reaction intermediates may offer new opportunities for rational drug design.
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*[[RmlC|RmlC]]
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== References ==
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==About this Structure==
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<references/>
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2IXL 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=2IXL OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation., Dong C, Major LL, Srikannathasan V, Errey JC, Giraud MF, Lam JS, Graninger M, Messner P, McNeil MR, Field RA, Whitfield C, Naismith JH, J Mol Biol. 2007 Jan 5;365(1):146-59. Epub 2006 Sep 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17046787 17046787]
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[[Category: Single protein]]
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[[Category: Streptococcus suis]]
[[Category: Streptococcus suis]]
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[[Category: dTDP-4-dehydrorhamnose 3,5-epimerase]]
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[[Category: Dong C]]
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[[Category: Dong, C.]]
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[[Category: Naismith JH]]
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[[Category: Naismith, J H.]]
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[[Category: NI]]
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[[Category: TRH]]
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[[Category: epimerase]]
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[[Category: epimerise]]
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[[Category: epimerize]]
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[[Category: isomerase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:34:41 2008''
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Current revision

RmlC S. suis with dTDP-rhamnose

PDB ID 2ixl

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