5wya

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==Structure of amino acid racemase, 2.65 A==
==Structure of amino acid racemase, 2.65 A==
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<StructureSection load='5wya' size='340' side='right' caption='[[5wya]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
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<StructureSection load='5wya' size='340' side='right'caption='[[5wya]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5wya]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WYA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WYA FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5wya]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lentilactobacillus_buchneri Lentilactobacillus buchneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WYA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WYA FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7VO:(2S,3S)-3-METHYL-2-[[2-METHYL-3-OXIDANYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLAMINO]PENTANOIC+ACID'>7VO</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wyf|5wyf]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7VO:(2S,3S)-3-METHYL-2-[[2-METHYL-3-OXIDANYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLAMINO]PENTANOIC+ACID'>7VO</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isoleucine_2-epimerase Isoleucine 2-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.21 5.1.1.21] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5wya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wya OCA], [https://pdbe.org/5wya PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wya RCSB], [https://www.ebi.ac.uk/pdbsum/5wya PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wya ProSAT]</span></td></tr>
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<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=5wya FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wya OCA], [http://pdbe.org/5wya PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wya RCSB], [http://www.ebi.ac.uk/pdbsum/5wya PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wya ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/ILE2E_LENBU ILE2E_LENBU]
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Crystal structures of Lactobacillus buchneri isoleucine 2-epimerase, a novel branched-chain amino-acid racemase, were determined for the enzyme in the apo form, in complex with pyridoxal 5'-phosphate (PLP), in complex with N-(5'-phosphopyridoxyl)-L-isoleucine (PLP-L-Ile) and in complex with N-(5'-phosphopyridoxyl)-D-allo-isoleucine (PLP-D-allo-Ile) at resolutions of 2.77, 1.94, 2.65 and 2.12 A, respectively. The enzyme assembled as a tetramer, with each subunit being composed of N-terminal, C-terminal and large PLP-binding domains. The active-site cavity in the apo structure was much more solvent-accessible than that in the PLP-bound structure. This indicates that a marked structural change occurs around the active site upon binding of PLP that provides a solvent-inaccessible environment for the enzymatic reaction. The main-chain coordinates of the L. buchneri isoleucine 2-epimerase monomer showed a notable similarity to those of alpha-amino--caprolactam racemase from Achromobactor obae and gamma-aminobutyrate aminotransferase from Escherichia coli. However, the amino-acid residues involved in substrate binding in those two enzymes are only partially conserved in L. buchneri isoleucine 2-epimerase, which may account for the differences in substrate recognition by the three enzymes. The structures bound with reaction-intermediate analogues (PLP-L-Ile and PLP-D-allo-Ile) and site-directed mutagenesis suggest that L-isoleucine epimerization proceeds through abstraction of the alpha-hydrogen of the substrate by Lys280, while Asp222 serves as the catalytic residue adding an alpha-hydrogen to the quinonoid intermediate to form D-allo-isoleucine.
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Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri.,Hayashi J, Mutaguchi Y, Minemura Y, Nakagawa N, Yoneda K, Ohmori T, Ohshima T, Sakuraba H Acta Crystallogr D Struct Biol. 2017 May 1;73(Pt 5):428-437. doi:, 10.1107/S2059798317005332. Epub 2017 Apr 19. PMID:28471367<ref>PMID:28471367</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5wya" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Isoleucine 2-epimerase]]
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[[Category: Large Structures]]
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[[Category: Hayashi, J]]
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[[Category: Lentilactobacillus buchneri]]
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[[Category: Mutaguchi, Y]]
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[[Category: Hayashi J]]
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[[Category: Ohshima, T]]
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[[Category: Mutaguchi Y]]
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[[Category: Sakuraba, H]]
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[[Category: Ohshima T]]
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[[Category: Fold type i]]
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[[Category: Sakuraba H]]
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[[Category: Isomerase]]
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[[Category: Plp-dependent enzyme]]
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Current revision

Structure of amino acid racemase, 2.65 A

PDB ID 5wya

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