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| ==The structure of dihydrodipicolinate synthase 2 from Arabidopsis thaliana in complex with (S)-lysine== | | ==The structure of dihydrodipicolinate synthase 2 from Arabidopsis thaliana in complex with (S)-lysine== |
| <StructureSection load='4dpq' size='340' side='right' caption='[[4dpq]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='4dpq' size='340' side='right'caption='[[4dpq]], [[Resolution|resolution]] 2.20Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4dpq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DPQ FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4dpq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DPQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DPQ FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.202Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dpp|4dpp]]</td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DHDPS2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=4dpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpq OCA], [https://pdbe.org/4dpq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dpq RCSB], [https://www.ebi.ac.uk/pdbsum/4dpq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dpq ProSAT]</span></td></tr> |
| <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </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=4dpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dpq OCA], [http://pdbe.org/4dpq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dpq RCSB], [http://www.ebi.ac.uk/pdbsum/4dpq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dpq ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/DAPA2_ARATH DAPA2_ARATH]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA) (By similarity). | | [https://www.uniprot.org/uniprot/DAPA2_ARATH DAPA2_ARATH] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA) (By similarity). |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| In plants, the lysine biosynthetic pathway is an attractive target for both the development of herbicides and increasing the nutritional value of crops given that lysine is a limiting amino acid in cereals. Dihydrodipicolinate synthase (DHDPS) and dihydrodipicolinate reductase (DHDPR) catalyse the first two committed steps of lysine biosynthesis. Here, we carry out for the first time a comprehensive characterisation of the structure and activity of both DHDPS and DHDPR from Arabidopsis thaliana. The A. thaliana DHDPS enzyme (At-DHDPS2) has similar activity to the bacterial form of the enzyme, but is more strongly allosterically inhibited by (S)-lysine. Structural studies of At-DHDPS2 show (S)-lysine bound at a cleft between two monomers, highlighting the allosteric site; however, unlike previous studies, binding is not accompanied by conformational changes, suggesting that binding may cause changes in protein dynamics rather than large conformation changes. DHDPR from A. thaliana (At-DHDPR2) has similar specificity for both NADH and NADPH during catalysis, and has tighter binding of substrate than has previously been reported. While all known bacterial DHDPR enzymes have a tetrameric structure, analytical ultracentrifugation, and scattering data unequivocally show that At-DHDPR2 exists as a dimer in solution. The exact arrangement of the dimeric protein is as yet unknown, but ab initio modelling of x-ray scattering data is consistent with an elongated structure in solution, which does not correspond to any of the possible dimeric pairings observed in the X-ray crystal structure of DHDPR from other organisms. This increased knowledge of the structure and function of plant lysine biosynthetic enzymes will aid future work aimed at improving primary production.
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| Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana.,Griffin MD, Billakanti JM, Wason A, Keller S, Mertens HD, Atkinson SC, Dobson RC, Perugini MA, Gerrard JA, Pearce FG PLoS One. 2012;7(7):e40318. doi: 10.1371/journal.pone.0040318. Epub 2012 Jul 5. PMID:22792278<ref>PMID:22792278</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4dpq" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| *[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]] | | *[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]] |
| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: 4-hydroxy-tetrahydrodipicolinate synthase]] | | [[Category: Arabidopsis thaliana]] |
| [[Category: Arath]] | | [[Category: Large Structures]] |
| [[Category: Billakanti, J M]] | | [[Category: Billakanti JM]] |
| [[Category: Dobson, R C.J]] | | [[Category: Dobson RCJ]] |
| [[Category: Gerrard, J A]] | | [[Category: Gerrard JA]] |
| [[Category: Griffin, M D.W]] | | [[Category: Griffin MDW]] |
| [[Category: Pearce, F G]] | | [[Category: Pearce FG]] |
| [[Category: Amino-acid biosynthesis]]
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| [[Category: Chloroplast]]
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| [[Category: Class i aldolase]]
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| [[Category: Lyase]]
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