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2z1z

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[[Image:2z1z.gif|left|200px]]
 
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{{Structure
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==Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana complexed with L-malate ion==
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|PDB= 2z1z |SIZE=350|CAPTION= <scene name='initialview01'>2z1z</scene>, resolution 2.40&Aring;
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<StructureSection load='2z1z' size='340' side='right'caption='[[2z1z]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MLT:MALATE+ION'>MLT</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5&#39;-PHOSPHATE'>PLP</scene>
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<table><tr><td colspan='2'>[[2z1z]] 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=2Z1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z1Z FirstGlance]. <br>
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|ACTIVITY= <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>
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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]] 2.4&#8491;</td></tr>
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|GENE= AT4g33680 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLT:D-MALATE'>MLT</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
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|DOMAIN=
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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=2z1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1z OCA], [https://pdbe.org/2z1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z1z RCSB], [https://www.ebi.ac.uk/pdbsum/2z1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z1z ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1z OCA], [http://www.ebi.ac.uk/pdbsum/2z1z PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2z1z RCSB]</span>
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== Function ==
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}}
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[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>
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== Evolutionary Conservation ==
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'''Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana complexed with L-malate ion'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z1/2z1z_consurf.spt"</scriptWhenChecked>
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The essential biosynthetic pathway to l-Lysine in bacteria and plants is an attractive target for the development of new antibiotics or herbicides because it is absent in humans, who must acquire this amino acid in their diet. Plants use a shortcut of a bacterial pathway to l-Lysine in which the pyridoxal-5'-phosphate (PLP)-dependent enzyme ll-diaminopimelate aminotransferase (LL-DAP-AT) transforms l-tetrahydrodipicolinic acid (L-THDP) directly to LL-DAP. In addition, LL-DAP-AT was recently found in Chlamydia sp., suggesting that inhibitors of this enzyme may also be effective against such organisms. In order to understand the mechanism of this enzyme and to assist in the design of inhibitors, the three-dimensional crystal structure of LL-DAP-AT was determined at 1.95 A resolution. The cDNA sequence of LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT) was optimized for expression in bacteria and cloned in Escherichia coli without its leader sequence but with a C-terminal hexahistidine affinity tag to aid protein purification. The structure of AtDAP-AT was determined using the multiple-wavelength anomalous dispersion (MAD) method with a seleno-methionine derivative. AtDAP-AT is active as a homodimer with each subunit having PLP in the active site. It belongs to the family of type I fold PLP-dependent enzymes. Comparison of the active site residues of AtDAP-AT and aspartate aminotransferases revealed that the PLP binding residues in AtDAP-AT are well conserved in both enzymes. However, Glu97* and Asn309* in the active site of AtDAP-AT are not found at similar positions in aspartate aminotransferases, suggesting that specific substrate recognition may require these residues from the other monomer. A malate-bound structure of AtDAP-AT allowed LL-DAP and L-glutamate to be modelled into the active site. These initial three-dimensional structures of LL-DAP-AT provide insight into its substrate specificity and catalytic mechanism.
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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2Z1Z is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z1Z OCA].
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z1z ConSurf].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia., Watanabe N, Cherney MM, van Belkum MJ, Marcus SL, Flegel MD, Clay MD, Deyholos MK, Vederas JC, James MN, J Mol Biol. 2007 Aug 17;371(3):685-702. Epub 2007 May 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17583737 17583737]
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<references/>
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__TOC__
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</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
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[[Category: LL-diaminopimelate aminotransferase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Cherney MM]]
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[[Category: Belkum, M J.van.]]
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[[Category: Clay MD]]
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[[Category: Cherney, M M.]]
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[[Category: Deyholos MK]]
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[[Category: Clay, M D.]]
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[[Category: Flegel MD]]
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[[Category: Deyholos, M K.]]
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[[Category: James MNG]]
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[[Category: Flegel, M D.]]
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[[Category: Marcus SL]]
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[[Category: James, M N.G.]]
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[[Category: Vederas JC]]
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[[Category: Marcus, S L.]]
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[[Category: Watanabe N]]
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[[Category: Vederas, J C.]]
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[[Category: Van Belkum MJ]]
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[[Category: Watanabe, N.]]
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[[Category: arabidopsis thaliana]]
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[[Category: ll-dap]]
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[[Category: ll-dap-at]]
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[[Category: ll-diaminopimelate aminotransferase]]
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[[Category: lysine biosynthesis]]
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[[Category: plp]]
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[[Category: thdpa]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:17:34 2008''
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Current revision

Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana complexed with L-malate ion

PDB ID 2z1z

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