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| | ==Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus== | | ==Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus== |
| - | <StructureSection load='2plk' size='340' side='right' caption='[[2plk]], [[Resolution|resolution]] 2.14Å' scene=''> | + | <StructureSection load='2plk' size='340' side='right'caption='[[2plk]], [[Resolution|resolution]] 2.14Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2plk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibvu Vibvu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PLK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2plk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus_CMCP6 Vibrio vulnificus CMCP6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PLK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P3D:(4-{(E)-[(5-AMINOPENTYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL+DIHYDROGEN+PHOSPHATE'>P3D</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]] 2.14Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2plj|2plj]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P3D:(4-{(E)-[(5-AMINOPENTYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL+DIHYDROGEN+PHOSPHATE'>P3D</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LysA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216895 VIBVU])</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=2plk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plk OCA], [https://pdbe.org/2plk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2plk RCSB], [https://www.ebi.ac.uk/pdbsum/2plk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2plk ProSAT]</span></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=2plk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plk OCA], [http://pdbe.org/2plk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2plk RCSB], [http://www.ebi.ac.uk/pdbsum/2plk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2plk ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibvu]] | + | [[Category: Large Structures]] |
| - | [[Category: Goldsmith, E J]] | + | [[Category: Vibrio vulnificus CMCP6]] |
| - | [[Category: Lee, J]] | + | [[Category: Goldsmith EJ]] |
| - | [[Category: Phillips, M A]] | + | [[Category: Lee J]] |
| - | [[Category: Beta barrel]] | + | [[Category: Phillips MA]] |
| - | [[Category: Beta/alpha barrel]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Type iv decarboxylase]]
| + | |
| Structural highlights
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The beta/alpha-barrel fold type basic amino acid decarboxylases include eukaryotic ornithine decarboxylases (ODC) and bacterial and plant enzymes with activity on L-arginine and meso-diaminopimelate. These enzymes catalyze essential steps in polyamine and lysine biosynthesis. Phylogenetic analysis suggests that diverse bacterial species also contain ODC-like enzymes from this fold type. However, in comparison with the eukaryotic ODCs, amino acid differences were identified in the sequence of the 3(10)-helix that forms a key specificity element in the active site, suggesting they might function on novel substrates. Putative decarboxylases from a phylogenetically diverse range of bacteria were characterized to determine their substrate preference. Enzymes from species within Methanosarcina, Pseudomonas, Bartonella, Nitrosomonas, Thermotoga, and Aquifex showed a strong preference for L-ornithine, whereas the enzyme from Vibrio vulnificus (VvL/ODC) had dual specificity functioning well on both L-ornithine and L-lysine. The x-ray structure of VvL/ODC was solved in the presence of the reaction products putrescine and cadaverine to 1.7 and 2.15A, respectively. The overall structure is similar to eukaryotic ODC; however, reorientation of the 3(10)-helix enlarging the substrate binding pocket allows L-lysine to be accommodated. The structure of the putrescine-bound enzyme suggests that a bridging water molecule between the shorter L-ornithine and key active site residues provides the structural basis for VvL/ODC to also function on this substrate. Our data demonstrate that there is greater structural and functional diversity in bacterial polyamine biosynthetic decarboxylases than previously suspected.
Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases.,Lee J, Michael AJ, Martynowski D, Goldsmith EJ, Phillips MA J Biol Chem. 2007 Sep 14;282(37):27115-25. Epub 2007 Jul 11. PMID:17626020[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lee J, Michael AJ, Martynowski D, Goldsmith EJ, Phillips MA. Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases. J Biol Chem. 2007 Sep 14;282(37):27115-25. Epub 2007 Jul 11. PMID:17626020 doi:http://dx.doi.org/10.1074/jbc.M704066200
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