4onv: Difference between revisions

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 ==Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate==
-<StructureSection load='4onv' size='340' side='right' caption='[[4onv]], [[Resolution|resolution]] 2.57&Aring;' scene=''>
+<StructureSection load='4onv' size='340' side='right'caption='[[4onv]], [[Resolution|resolution]] 2.57&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4onv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ONV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ONV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4onv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ONV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ONV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</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]] 2.57&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4onv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4onv OCA], [http://pdbe.org/4onv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4onv RCSB], [http://www.ebi.ac.uk/pdbsum/4onv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4onv ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</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=4onv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4onv OCA], [https://pdbe.org/4onv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4onv RCSB], [https://www.ebi.ac.uk/pdbsum/4onv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4onv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YAGE_ECOLI YAGE_ECOLI]] Catalyzes the formation of 2-keto-3-deoxy-galactonate (KDGal) from pyruvate and glyceraldehyde. Overexpression leads to increased growth (over 2 hours) in the presence of the antibiotics norfloxacin, ampicillin and streptomycin.
+[https://www.uniprot.org/uniprot/YAGE_ECOLI YAGE_ECOLI] Catalyzes the formation of 2-keto-3-deoxy-galactonate (KDGal) from pyruvate and glyceraldehyde. Overexpression leads to increased growth (over 2 hours) in the presence of the antibiotics norfloxacin, ampicillin and streptomycin.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-YagE is a 33 kDa prophage protein encoded by CP4-6 prophage element in Escherichia coli K12 genome. Here, we report the structures of YagE complexes with pyruvate (PDB Id 3N2X) and KDGal (2-keto-3-deoxy galactonate) (PDB Id 3NEV) at 2.2A resolution. Pyruvate depletion assay in presence of glyceraldehyde shows that YagE catalyses the aldol condensation of pyruvate and glyceraldehyde. Our results indicate that the biochemical function of YagE is that of a 2-keto-3-deoxy gluconate (KDG) aldolase. Interestingly, E. coli K12 genome lacks an intrinsic KDG aldolase. Moreover, the over-expression of YagE increases cell viability in the presence of certain bactericidal antibiotics, indicating a putative biological role of YagE as a prophage encoded virulence factor enabling the survival of bacteria in the presence of certain antibiotics. The analysis implies a possible mechanism of antibiotic resistance conferred by the over-expression of prophage encoded YagE to E. coli. Proteins 2011, (c) 2011 Wiley-Liss, Inc.
-Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis.,Bhaskar V, Kumar M, Manicka S, Tripathi S, Venkatraman A, Krishnaswamy S Proteins. 2011 Apr;79(4):1132-42. doi: 10.1002/prot.22949. Epub 2011 Feb, 3. PMID:21294156<ref>PMID:21294156</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4onv" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bhaskar, V]]
+[[Category: Escherichia coli K-12]]
-[[Category: Krishnaswamy, S]]
+[[Category: Large Structures]]
-[[Category: Kumar, P Manoj]]
+[[Category: Bhaskar V]]
-[[Category: Manicka, S]]
+[[Category: Krishnaswamy S]]
-[[Category: Aldolase class i]]
+[[Category: Manicka S]]
-[[Category: Lyase]]
+[[Category: Manoj Kumar P]]
-[[Category: Nal superfamily]]
-[[Category: Tim barrel]]