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| | ==Structure of amino acid racemase, 2.12 A== | | ==Structure of amino acid racemase, 2.12 A== |
| - | <StructureSection load='5wyf' size='340' side='right' caption='[[5wyf]], [[Resolution|resolution]] 2.12Å' scene=''> | + | <StructureSection load='5wyf' size='340' side='right'caption='[[5wyf]], [[Resolution|resolution]] 2.12Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5wyf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WYF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5wyf]] 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=5WYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WYF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=ILP:N-[O-PHOSPHONO-PYRIDOXYL]-ISOLEUCINE'>ILP</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]] 2.12Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wya|5wya]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=ILP:N-[O-PHOSPHONO-PYRIDOXYL]-ISOLEUCINE'>ILP</scene></td></tr> |
| - | <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>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5wyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wyf OCA], [https://pdbe.org/5wyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wyf RCSB], [https://www.ebi.ac.uk/pdbsum/5wyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wyf 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=5wyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wyf OCA], [http://pdbe.org/5wyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wyf RCSB], [http://www.ebi.ac.uk/pdbsum/5wyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wyf ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ILE2E_LENBU ILE2E_LENBU] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Isoleucine 2-epimerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Hayashi, J]] | + | [[Category: Lentilactobacillus buchneri]] |
| - | [[Category: Mutaguchi, Y]] | + | [[Category: Hayashi J]] |
| - | [[Category: Ohshima, T]] | + | [[Category: Mutaguchi Y]] |
| - | [[Category: Sakuraba, H]] | + | [[Category: Ohshima T]] |
| - | [[Category: Fold type i]]
| + | [[Category: Sakuraba H]] |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Plp-dependent enzyme]]
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| Structural highlights
Function
ILE2E_LENBU
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hayashi J, Mutaguchi Y, Minemura Y, Nakagawa N, Yoneda K, Ohmori T, Ohshima T, Sakuraba H. Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri. Acta Crystallogr D Struct Biol. 2017 May 1;73(Pt 5):428-437. doi:, 10.1107/S2059798317005332. Epub 2017 Apr 19. PMID:28471367 doi:http://dx.doi.org/10.1107/S2059798317005332
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