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| | ==Crystal structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12 in complex with pyruvate== | | ==Crystal structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12 in complex with pyruvate== |
| - | <StructureSection load='3n2x' size='340' side='right' caption='[[3n2x]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3n2x' size='340' side='right'caption='[[3n2x]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3n2x]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N2X FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3n2x]] 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=3N2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N2X 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></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]] 2.2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MCL:NZ-(1-CARBOXYETHYL)-LYSINE'>MCL</scene></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=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2v8z|2v8z]], [[2v9d|2v9d]]</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=3n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n2x OCA], [https://pdbe.org/3n2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n2x RCSB], [https://www.ebi.ac.uk/pdbsum/3n2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n2x ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0268, JW0261, yagE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
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| - | <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=3n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n2x OCA], [http://pdbe.org/3n2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n2x RCSB], [http://www.ebi.ac.uk/pdbsum/3n2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n2x ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Bhaskar, V]] | + | [[Category: Large Structures]] |
| - | [[Category: Krishnaswamy, S]] | + | [[Category: Bhaskar V]] |
| - | [[Category: Kumar, P M]] | + | [[Category: Krishnaswamy S]] |
| - | [[Category: Manicka, S]]
| + | [[Category: Kumar PM]] |
| - | [[Category: Aldolase]] | + | [[Category: Manicka S]] |
| - | [[Category: Lyase]] | + | |
| - | [[Category: Protein-ligand complex]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bhaskar V, Kumar M, Manicka S, Tripathi S, Venkatraman A, Krishnaswamy S. Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis. Proteins. 2011 Apr;79(4):1132-42. doi: 10.1002/prot.22949. Epub 2011 Feb, 3. PMID:21294156 doi:10.1002/prot.22949
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