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| | ==Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP== | | ==Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP== |
| - | <StructureSection load='3ekm' size='340' side='right' caption='[[3ekm]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='3ekm' size='340' side='right'caption='[[3ekm]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ekm]] is a 6 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=3EKM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EKM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ekm]] is a 6 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=3EKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EKM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZDR:(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC+ACID'>ZDR</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ejx|3ejx]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZDR:(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC+ACID'>ZDR</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapF ([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=3ekm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ekm OCA], [https://pdbe.org/3ekm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ekm RCSB], [https://www.ebi.ac.uk/pdbsum/3ekm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ekm 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/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </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=3ekm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ekm OCA], [http://pdbe.org/3ekm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ekm RCSB], [http://www.ebi.ac.uk/pdbsum/3ekm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ekm ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DAPF_ARATH DAPF_ARATH]] Racemase that operates by a 'two-base' mechanism, which involves one active-site cysteine acting as a base to abstract the alpha-proton of an amino acid, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face.<ref>PMID:15652176</ref> | + | [https://www.uniprot.org/uniprot/DAPF_ARATH DAPF_ARATH] Racemase that operates by a 'two-base' mechanism, which involves one active-site cysteine acting as a base to abstract the alpha-proton of an amino acid, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face.<ref>PMID:15652176</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Diaminopimelate epimerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Belkum, M J.van]]
| + | [[Category: Cherney MM]] |
| - | [[Category: Cherney, M M]] | + | [[Category: James MNG]] |
| - | [[Category: James, M N.G]] | + | [[Category: Moorthie VA]] |
| - | [[Category: Moorthie, V A]] | + | [[Category: Pillai B]] |
| - | [[Category: Pillai, B]] | + | [[Category: Vederas JC]] |
| - | [[Category: Vederas, J C]] | + | [[Category: Van Belkum MJ]] |
| - | [[Category: Arabidopsis]] | + | |
| - | [[Category: Aziridino-diaminopimelate]]
| + | |
| - | [[Category: Catalytic mechanism]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Plp-independent amino acid racemase]]
| + | |
| Structural highlights
Function
DAPF_ARATH Racemase that operates by a 'two-base' mechanism, which involves one active-site cysteine acting as a base to abstract the alpha-proton of an amino acid, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Diaminopimelate (DAP) epimerase is a key enzyme for the biosynthesis of lysine in plants. Lysine is an essential dietary nutrient for mammals. In both plants and bacteria, DAP epimerase catalyzes the interconversion of LL-DAP and DL(meso)-DAP. The absence of a mammalian homolog makes DAP epimerase a promising target for the design of novel herbicides and antibacterials. This enzyme requires no cofactors and it functions through an unusual mechanism involving two cysteine residues acting in concert and alternating as a base (thiolate) and as an acid (thiol). The present study reports the crystal structures of two enzyme-inhibitor complexes of DAP epimerase from Arabidopsis thaliana with different isomers of the irreversible inhibitor and substrate mimic, 2-(4-amino-4-carboxybutyl)-aziridine-2-carboxylate, at 1.95 and 2.3 A resolution. These structures provide the first atomic details of a plant amino acid racemase. Structural analysis reveals that ligand binding to a cleft between the two domains of the enzyme is accompanied by domain closure with two strictly conserved cysteine residues, Cys99 and Cys254, optimally positioned to perform acid/base catalysis via a carbanion stabilization mechanism on the stereogenic alpha-carbon atom of the amino acid. Stereochemical control in catalysis is achieved by means of a highly symmetric catalytic site that can accommodate both the L and D stereogenic centers of DAP at the proximal site, whereas specific interactions at the distal site require only the L configuration. Structural comparisons of the plant enzyme with its bacterial counterpart from Haemophilus influenzae reveal significant conservation of amino acid residues around the active site that extends to their three-dimensional structures and catalytic mechanism.
Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis.,Pillai B, Moorthie VA, van Belkum MJ, Marcus SL, Cherney MM, Diaper CM, Vederas JC, James MN J Mol Biol. 2009 Jan 16;385(2):580-94. Epub 2008 Nov 5. PMID:19013471[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hudson AO, Bless C, Macedo P, Chatterjee SP, Singh BK, Gilvarg C, Leustek T. Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways. Biochim Biophys Acta. 2005 Jan 18;1721(1-3):27-36. Epub 2004 Nov 4. PMID:15652176 doi:http://dx.doi.org/S0304-4165(04)00243-0
- ↑ Pillai B, Moorthie VA, van Belkum MJ, Marcus SL, Cherney MM, Diaper CM, Vederas JC, James MN. Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis. J Mol Biol. 2009 Jan 16;385(2):580-94. Epub 2008 Nov 5. PMID:19013471 doi:10.1016/j.jmb.2008.10.072
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