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| | ==Complex structure of a broad specificity amino acid racemase (Bar) within the reactive intermediate== | | ==Complex structure of a broad specificity amino acid racemase (Bar) within the reactive intermediate== |
| - | <StructureSection load='4fs9' size='340' side='right' caption='[[4fs9]], [[Resolution|resolution]] 3.10Å' scene=''> | + | <StructureSection load='4fs9' size='340' side='right'caption='[[4fs9]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fs9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FS9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fs9]] 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=4FS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FS9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PE1:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-LYSINE'>PE1</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]] 3.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dyj|4dyj]], [[4dza|4dza]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PE1:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-LYSINE'>PE1</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Amino-acid_racemase Amino-acid racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.10 5.1.1.10] </span></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=4fs9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fs9 OCA], [https://pdbe.org/4fs9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fs9 RCSB], [https://www.ebi.ac.uk/pdbsum/4fs9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fs9 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=4fs9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fs9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fs9 RCSB], [http://www.ebi.ac.uk/pdbsum/4fs9 PDBsum]</span></td></tr> | + | |
| | </table> | | </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:22806802, PubMed:23118975).<ref>PMID:22806802</ref> <ref>PMID:23118975</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4fs9" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Amino-acid racemase]] | + | [[Category: Large Structures]] |
| | [[Category: Pseudomonas putida]] | | [[Category: Pseudomonas putida]] |
| - | [[Category: Wang, W C]] | + | [[Category: Wang WC]] |
| - | [[Category: Wu, H M]] | + | [[Category: Wu HM]] |
| - | [[Category: Isomerase]]
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| - | [[Category: Plp binding]]
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| - | [[Category: Racemization]]
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| Structural highlights
Function
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:22806802, PubMed:23118975).[1] [2]
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Liu JL, Liu XQ, Shi YW. Expression, purification, and characterization of alanine racemase from Pseudomonas putida YZ-26. World J Microbiol Biotechnol. 2012 Jan;28(1):267-74. doi:, 10.1007/s11274-011-0816-1. Epub 2011 Jun 21. PMID:22806802 doi:http://dx.doi.org/10.1007/s11274-011-0816-1
- ↑ Wu HM, Kuan YC, Chu CH, Hsu WH, Wang WC. Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants. PLoS One. 2012;7(10):e48301. doi: 10.1371/journal.pone.0048301. Epub 2012 Oct 31. PMID:23118975 doi:http://dx.doi.org/10.1371/journal.pone.0048301
- ↑ Wu HM, Kuan YC, Chu CH, Hsu WH, Wang WC. Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants. PLoS One. 2012;7(10):e48301. doi: 10.1371/journal.pone.0048301. Epub 2012 Oct 31. PMID:23118975 doi:http://dx.doi.org/10.1371/journal.pone.0048301
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