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4dza

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Revision as of 08:44, 21 September 2022

Crystal structure of a lysine racemase within internal aldimine linkage

Structural highlights

4dza is a 1 chain structure with sequence from Proteus mirabilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[LYR_PROMI] Amino-acid racemase that catalyzes the interconversion of L-lysine and D-lysine. To a lesser extent, is also able to interconvert arginine enantiomers (Ref.1, PubMed:23118975). Cannot use methionine, asparagine, alanine, leucine, glutamine, phenylalanine and histidine as substrates (Ref.1).^[1] [UniProtKB:I0J1I6]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4dza"

Categories: Large Structures | Proteus mirabilis | Wang WC | Wu HM

@@ Line 3: / Line 3: @@
 <StructureSection load='4dza' size='340' side='right'caption='[[4dza]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4dza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29906 Atcc 29906]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DZA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4dza]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DZA FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysine_racemase Lysine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.5 5.1.1.5] </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=4dza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dza OCA], [https://pdbe.org/4dza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dza RCSB], [https://www.ebi.ac.uk/pdbsum/4dza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dza 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=4dza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dza OCA], [http://pdbe.org/4dza PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dza RCSB], [http://www.ebi.ac.uk/pdbsum/4dza PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dza ProSAT]</span></td></tr>
 </table>
+== Function ==
+[[https://www.uniprot.org/uniprot/LYR_PROMI LYR_PROMI]] Amino-acid racemase that catalyzes the interconversion of L-lysine and D-lysine. To a lesser extent, is also able to interconvert arginine enantiomers (Ref.1, PubMed:23118975). Cannot use methionine, asparagine, alanine, leucine, glutamine, phenylalanine and histidine as substrates (Ref.1).<ref>PMID:23118975</ref> [UniProtKB:I0J1I6]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 29906]]
 [[Category: Large Structures]]
-[[Category: Lysine racemase]]
+[[Category: Proteus mirabilis]]
-[[Category: Wang, W C]]
+[[Category: Wang WC]]
-[[Category: Wu, H M]]
+[[Category: Wu HM]]
-[[Category: Isomerase]]
-[[Category: Plp binding]]
-[[Category: Racemization]]

4dza

From Proteopedia

Revision as of 08:44, 21 September 2022

Crystal structure of a lysine racemase within internal aldimine linkage

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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