2dtj: Difference between revisions

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-[[Image:2dtj.jpg|left|200px]]<br /><applet load="2dtj" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2dtj, resolution 1.58&Aring;" />
-'''Crystal structure of regulatory subunit of aspartate kinase from Corynebacterium glutamicum'''<br />
-==Overview==
+==Crystal structure of regulatory subunit of aspartate kinase from Corynebacterium glutamicum==
-Aspartate kinase (AK) catalyzes the first step of the biosynthesis of the, aspartic acid family amino acids, and is regulated via feedback inhibition, by end-products including Thr and Lys. To elucidate the mechanism of this, inhibition, we determined the crystal structure of the regulatory subunit, of AK from Corynebacterium glutamicum at 1.58 A resolution in the, Thr-binding form, the first crystal structure of the regulatory subunit of, alpha(2)beta(2)-type AK. The regulatory subunit contains two ACT domain, motifs per monomer and is arranged as a dimer. Two non-equivalent ACT, domains from different chains form an effector-binding unit that binds a, single Thr molecule, and the resulting two effector-binding units of the, dimer associate perpendicularly in a face-to-face manner. The regulatory, subunit is a monomer in the absence of Thr but becomes a dimer by adding, Thr. The dimerization is eliminated in mutant AKs with changes in the, Thr-binding region, suggesting that the dimerization induced by Thr, binding is a key step in the inhibitory mechanism of AK from C., glutamicum. A putative Lys-binding site and the inhibitory mechanism of, CgAK are discussed.
+<StructureSection load='2dtj' size='340' side='right'caption='[[2dtj]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2dtj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTJ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.58&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=THR:THREONINE'>THR</scene></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=2dtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dtj OCA], [https://pdbe.org/2dtj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dtj RCSB], [https://www.ebi.ac.uk/pdbsum/2dtj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dtj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AK_CORGL AK_CORGL] Catalyzes the phosphorylation of the beta-carboxyl group of aspartic acid with ATP to yield 4-phospho-L-aspartate, which is involved in the branched biosynthetic pathway leading to the biosynthesis of amino acids lysine, threonine, isoleucine and methionine.<ref>PMID:17350037</ref> <ref>PMID:20573952</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dt/2dtj_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2dtj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Aspartate kinase (AK) catalyzes the first step of the biosynthesis of the aspartic acid family amino acids, and is regulated via feedback inhibition by end-products including Thr and Lys. To elucidate the mechanism of this inhibition, we determined the crystal structure of the regulatory subunit of AK from Corynebacterium glutamicum at 1.58 A resolution in the Thr-binding form, the first crystal structure of the regulatory subunit of alpha(2)beta(2)-type AK. The regulatory subunit contains two ACT domain motifs per monomer and is arranged as a dimer. Two non-equivalent ACT domains from different chains form an effector-binding unit that binds a single Thr molecule, and the resulting two effector-binding units of the dimer associate perpendicularly in a face-to-face manner. The regulatory subunit is a monomer in the absence of Thr but becomes a dimer by adding Thr. The dimerization is eliminated in mutant AKs with changes in the Thr-binding region, suggesting that the dimerization induced by Thr binding is a key step in the inhibitory mechanism of AK from C. glutamicum. A putative Lys-binding site and the inhibitory mechanism of CgAK are discussed.
-==About this Structure==
+Structural Insight into concerted inhibition of alpha 2 beta 2-type aspartate kinase from Corynebacterium glutamicum.,Yoshida A, Tomita T, Kurihara T, Fushinobu S, Kuzuyama T, Nishiyama M J Mol Biol. 2007 Apr 27;368(2):521-36. Epub 2007 Feb 20. PMID:17350037<ref>PMID:17350037</ref>
-DTJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum] with <scene name='pdbligand=THR:'>THR</scene> and <scene name='pdbligand=CIT:'>CIT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aspartate_kinase Aspartate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.4 2.7.2.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTJ OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural Insight into Concerted Inhibition of alpha(2)beta(2)-Type Aspartate Kinase from Corynebacterium glutamicum., Yoshida A, Tomita T, Kurihara T, Fushinobu S, Kuzuyama T, Nishiyama M, J Mol Biol. 2007 Apr 27;368(2):521-36. Epub 2007 Feb 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17350037 17350037]
+</div>
-[[Category: Aspartate kinase]]
+<div class="pdbe-citations 2dtj" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Corynebacterium glutamicum]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Fushinobu, S.]]
+[[Category: Fushinobu S]]
-[[Category: Kuzuyama, T.]]
+[[Category: Kuzuyama T]]
-[[Category: Nishiyama, M.]]
+[[Category: Nishiyama M]]
-[[Category: Tomita, T.]]
+[[Category: Tomita T]]
-[[Category: Yoshida, A.]]
+[[Category: Yoshida A]]
-[[Category: CIT]]
-[[Category: THR]]
-[[Category: protein-ligand complex]]
-[[Category: regulatory subunit]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:26:31 2008''