3ryk: Difference between revisions

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 <StructureSection load='3ryk' size='340' side='right'caption='[[3ryk]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ryk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_(strain_ames) Bacillus anthracis (strain ames)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RYK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ryk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_str._Ames Bacillus anthracis str. Ames]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RYK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.631&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BAS1136, BA_1229, GBAA_1229, rfbC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198094 Bacillus anthracis (strain Ames)])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_3,5-epimerase dTDP-4-dehydrorhamnose 3,5-epimerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.13 5.1.3.13] </span></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=3ryk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ryk OCA], [https://pdbe.org/3ryk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ryk RCSB], [https://www.ebi.ac.uk/pdbsum/3ryk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ryk ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/A0A6L7H6N0_BACAN A0A6L7H6N0_BACAN] 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.[RuleBase:RU364069]
-The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes (RfbA, RfbB, RfbC and RfbD) and is an attractive drug target because there are no homologs in mammals. It was found that co-purifying and screening RfbC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) from B. anthracis in the presence of the other three B. anthracis enzymes of the biosynthetic pathway yielded crystals that were suitable for data collection. RfbC crystallized as a dimer and its structure was determined at 1.63 A resolution. Two different ligands were bound in the protein structure: pyrophosphate in the active site of one monomer and dTDP in the other monomer. A structural comparison with RfbC homologs showed that the key active-site residues are conserved across kingdoms.
-Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme dTDP-4-dehydrorhamnose 3,5-epimerase (RfbC).,Shornikov A, Tran H, Macias J, Halavaty AS, Minasov G, Anderson WF, Kuhn ML Acta Crystallogr F Struct Biol Commun. 2017 Dec 1;73(Pt 12):664-671. doi:, 10.1107/S2053230X17015849. Epub 2017 Nov 10. PMID:29199987<ref>PMID:29199987</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3ryk" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[RmlC|RmlC]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Bacillus anthracis str. Ames]]
 [[Category: Large Structures]]
-[[Category: DTDP-4-dehydrorhamnose 3,5-epimerase]]
+[[Category: Anderson WF]]
-[[Category: Anderson, W F]]
+[[Category: Halavaty AS]]
-[[Category: Structural genomic]]
+[[Category: Kuhn M]]
-[[Category: Halavaty, A S]]
+[[Category: Kwon K]]
-[[Category: Kuhn, M]]
+[[Category: Minasov G]]
-[[Category: Kwon, K]]
+[[Category: Shuvalova L]]
-[[Category: Minasov, G]]
-[[Category: Shuvalova, L]]
-[[Category: 5-epimerase]]
-[[Category: Dtdp-4-dehydrorhamnose 3]]
-[[Category: Infectious disease]]
-[[Category: Isomerase]]
-[[Category: Jelly roll-like topology]]
-[[Category: Rhamnose pathway]]
-[[Category: The 3 and 5 positions of the sugar ring]]
-[[Category: The enzyme epimerizes at two carbon center]]