4dyj

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Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage

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Categories: Large Structures | Pseudomonas putida | Wang WC | Wu HM

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[4dyj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.45&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4dyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dyj OCA], [https://pdbe.org/4dyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dyj RCSB], [https://www.ebi.ac.uk/pdbsum/4dyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dyj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/BSR_PSEPU BSR_PSEPU]] Amino-acid racemase that catalyzes the interconversion of L-lysine and D-lysine, and L-arginine and D-arginine (PubMed:23118975). To a lesser extent, is also able to interconvert alanine and isoleucine enantiomers (PubMed:23118975, PubMed:22806802).<ref>PMID:22806802</ref> <ref>PMID:23118975</ref>
+[https://www.uniprot.org/uniprot/BSR_PSEPU BSR_PSEPU] Amino-acid racemase that catalyzes the interconversion of L-lysine and D-lysine, and L-arginine and D-arginine (PubMed:23118975). To a lesser extent, is also able to interconvert alanine and isoleucine enantiomers (PubMed:23118975, PubMed:22806802).<ref>PMID:22806802</ref> <ref>PMID:23118975</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Lysine racemase, a pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase that catalyzes the interconversion of lysine enantiomers, is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants. Here, we have determined the first crystal structure of a lysine racemase (Lyr) from Proteus mirabilis BCRC10725, which shows the highest activity toward lysine and weaker activity towards arginine. In addition, we establish the first broad-specificity amino acid racemase (Bar) structure from Pseudomonas putida DSM84, which presents not only the highest activity toward lysine but also remarkably broad substrate specificity. A complex structure of Bar-lysine is also established here. These structures demonstrate the similar fold of alanine racemase, which is a head-to-tail homodimer with each protomer containing an N-terminal (alpha/beta)(8) barrel and a C-terminal beta-stranded domain. The active-site residues are located at the protomer interface that is a funnel-like cavity with two catalytic bases, one from each protomer, and the PLP binding site is at the bottom of this cavity. Structural comparisons, site-directed mutagenesis, kinetic, and modeling studies identify a conserved arginine and an adjacent conserved asparagine that fix the orientation of the PLP O3 atom in both structures and assist in the enzyme activity. Furthermore, side chains of two residues in alpha-helix 10 have been discovered to point toward the cavity and define the substrate specificity. Our results provide a structural foundation for the design of racemases with pre-determined substrate specificity and for the development of the non-antibiotic selection system in transgenic plants.
-Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants.,Wu HM, Kuan YC, Chu CH, Hsu WH, Wang WC PLoS One. 2012;7(10):e48301. doi: 10.1371/journal.pone.0048301. Epub 2012 Oct 31. PMID:23118975<ref>PMID:23118975</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4dyj" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

4dyj

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Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage

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