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| | ==Crystal structure of apo-LL-diaminopimelate aminotransferase from Arabidopsis thaliana (no PLP)== | | ==Crystal structure of apo-LL-diaminopimelate aminotransferase from Arabidopsis thaliana (no PLP)== |
| - | <StructureSection load='3ei7' size='340' side='right' caption='[[3ei7]], [[Resolution|resolution]] 1.99Å' scene=''> | + | <StructureSection load='3ei7' size='340' side='right'caption='[[3ei7]], [[Resolution|resolution]] 1.99Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ei7]] 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=3EI7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EI7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ei7]] 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=3EI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EI7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.99Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ei5|3ei5]], [[3ei6|3ei6]], [[3ei8|3ei8]], [[3ei9|3ei9]], [[3eia|3eia]], [[3eib|3eib]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DAP, AGD2, At4g33680, T16L1.170 ([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=3ei7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ei7 OCA], [https://pdbe.org/3ei7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ei7 RCSB], [https://www.ebi.ac.uk/pdbsum/3ei7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ei7 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/LL-diaminopimelate_aminotransferase LL-diaminopimelate aminotransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.83 2.6.1.83] </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=3ei7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ei7 OCA], [http://pdbe.org/3ei7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ei7 RCSB], [http://www.ebi.ac.uk/pdbsum/3ei7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ei7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DAPAT_ARATH DAPAT_ARATH]] Required for lysine biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate, a reaction that requires three enzymes in E.coli. Not active with meso-diaminopimelate, lysine or ornithine as substrates.<ref>PMID:16361515</ref> <ref>PMID:21435399</ref> | + | [https://www.uniprot.org/uniprot/DAPAT_ARATH DAPAT_ARATH] Required for lysine biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate, a reaction that requires three enzymes in E.coli. Not active with meso-diaminopimelate, lysine or ornithine as substrates.<ref>PMID:16361515</ref> <ref>PMID:21435399</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: LL-diaminopimelate aminotransferase]] | |
| - | [[Category: Belkum, M J.van]] | |
| - | [[Category: Cherney, M M]] | |
| - | [[Category: Clay, M D]] | |
| - | [[Category: James, M N.G]] | |
| - | [[Category: Vederas, J C]] | |
| - | [[Category: Watanabe, N]] | |
| - | [[Category: Aminotransferase]] | |
| | [[Category: Arabidopsis thaliana]] | | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Chloroplast]] | + | [[Category: Large Structures]] |
| - | [[Category: Ll-diaminopimelate]] | + | [[Category: Cherney MM]] |
| - | [[Category: Lysine biosynthesis]] | + | [[Category: Clay MD]] |
| - | [[Category: Plastid]] | + | [[Category: James MNG]] |
| - | [[Category: Pyridoxal 5' phosphate]] | + | [[Category: Vederas JC]] |
| - | [[Category: Pyridoxal phosphate]] | + | [[Category: Watanabe N]] |
| - | [[Category: Transferase]] | + | [[Category: Van Belkum MJ]] |
| - | [[Category: Transit peptide]]
| + | |
| Structural highlights
Function
DAPAT_ARATH Required for lysine biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate, a reaction that requires three enzymes in E.coli. Not active with meso-diaminopimelate, lysine or ornithine as substrates.[1] [2]
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
LL-Diaminopimelate aminotransferase (LL-DAP-AT), a pyridoxal phosphate (PLP)-dependent enzyme in the lysine biosynthetic pathways of plants and Chlamydia, is a potential target for the development of herbicides or antibiotics. This homodimeric enzyme converts L-tetrahydrodipicolinic acid (THDP) directly to LL-DAP using L-glutamate as the source of the amino group. Earlier, we described the 3D structures of native and malate-bound LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT). Seven additional crystal structures of AtDAP-AT and its variants are reported here as part of an investigation into the mechanism of substrate recognition and catalysis. Two structures are of AtDAP-AT with reduced external aldimine analogues: N-(5'-phosphopyridoxyl)-L-glutamate (PLP-Glu) and N-(5'-phosphopyridoxyl)- LL-Diaminopimelate (PLP-DAP) bound in the active site. Surprisingly, they reveal that both L-glutamate and LL-DAP are recognized in a very similar fashion by the same sets of amino acid residues; both molecules adopt twisted V-shaped conformations. With both substrates, the alpha-carboxylates are bound in a salt bridge with Arg404, whereas the distal carboxylates are recognized via hydrogen bonds to the well-conserved side chains of Tyr37, Tyr125 and Lys129. The distal C(epsilon) amino group of LL-DAP is specifically recognized by several non-covalent interactions with residues from the other subunit (Asn309*, Tyr94*, Gly95*, and Glu97* (Amino acid designators followed by an asterisk (*) indicate that the residues originate in the other subunit of the dimer)) and by three bound water molecules. Two catalytically inactive variants of AtDAP-AT were created via site-directed mutagenesis of the active site lysine (K270N and K270Q). The structures of these variants permitted the observation of the unreduced external aldimines of PLP with L-glutamate and with LL-DAP in the active site, and revealed differences in the torsion angle about the PLP-substrate bond. Lastly, an apo-AtDAP-AT structure missing PLP revealed details of conformational changes induced by PLP binding and substrate entry into the active site.
Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana.,Watanabe N, Clay MD, van Belkum MJ, Cherney MM, Vederas JC, James MN J Mol Biol. 2008 Dec 31;384(5):1314-29. Epub 2008 Oct 15. PMID:18952095[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hudson AO, Singh BK, Leustek T, Gilvarg C. An LL-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants. Plant Physiol. 2006 Jan;140(1):292-301. Epub 2005 Dec 16. PMID:16361515 doi:http://dx.doi.org/pp.105.072629
- ↑ Watanabe N, James MN. Structural insights for the substrate recognition mechanism of LL-diaminopimelate aminotransferase. Biochim Biophys Acta. 2011 Nov;1814(11):1528-33. doi:, 10.1016/j.bbapap.2011.03.008. Epub 2011 Mar 22. PMID:21435399 doi:http://dx.doi.org/10.1016/j.bbapap.2011.03.008
- ↑ Watanabe N, Clay MD, van Belkum MJ, Cherney MM, Vederas JC, James MN. Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana. J Mol Biol. 2008 Dec 31;384(5):1314-29. Epub 2008 Oct 15. PMID:18952095 doi:http://dx.doi.org/10.1016/j.jmb.2008.10.022
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