2plj: Difference between revisions
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|PDB= 2plj |SIZE=350|CAPTION= <scene name='initialview01'>2plj</scene>, resolution 1.70Å | |PDB= 2plj |SIZE=350|CAPTION= <scene name='initialview01'>2plj</scene>, resolution 1.70Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P3T:(4-{[(4-AMINOBUTYL)AMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL+DIHYDROGEN+PHOSPHATE'>P3T</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= LysA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=672 Vibrio vulnificus]) | |GENE= LysA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=672 Vibrio vulnificus]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[2plk|2PLK]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2plj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plj OCA], [http://www.ebi.ac.uk/pdbsum/2plj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2plj RCSB]</span> | |||
}} | }} | ||
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[[Category: Lee, J.]] | [[Category: Lee, J.]] | ||
[[Category: Phillips, M A.]] | [[Category: Phillips, M A.]] | ||
[[Category: beta barrel]] | [[Category: beta barrel]] | ||
[[Category: beta/alpha barrel]] | [[Category: beta/alpha barrel]] | ||
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[[Category: type iv decarboxylase]] | [[Category: type iv decarboxylase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:37:35 2008'' | ||
Revision as of 04:37, 31 March 2008
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| , resolution 1.70Å | |||||||
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| Ligands: | , | ||||||
| Gene: | LysA (Vibrio vulnificus) | ||||||
| Related: | 2PLK
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of lysine/ornithine decarboxylase complexed with putrescine from Vibrio vulnificus
OverviewOverview
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.
About this StructureAbout this Structure
2PLJ is a Single protein structure of sequence from Vibrio vulnificus. Full crystallographic information is available from OCA.
ReferenceReference
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
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