3a9i: Difference between revisions

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-{{Seed}}
-[[Image:3a9i.jpg|left|200px]]
-<!--
+==Crystal structure of homocitrate synthase from Thermus thermophilus complexed with Lys==
-The line below this paragraph, containing "STRUCTURE_3a9i", creates the "Structure Box" on the page.
+<StructureSection load='3a9i' size='340' side='right'caption='[[3a9i]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3a9i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A9I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A9I FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene></td></tr>
-{{STRUCTURE_3a9i|  PDB=3a9i  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a9i OCA], [https://pdbe.org/3a9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a9i RCSB], [https://www.ebi.ac.uk/pdbsum/3a9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a9i ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HOSA_THET2 HOSA_THET2] Catalyzes the aldol-type condensation of 2-oxoglutarate with acetyl-CoA to yield homocitrate (PubMed:19996101, PubMed:12095615). Carries out the first step of the alpha-aminoadipate (AAA) lysine biosynthesis pathway (PubMed:9868782). To a lesser extent, can also use oxaloacetate in place of 2-oxoglutarate, leading to citrate. Does not display 2-isopropylmalate synthase activity since it cannot use 2-oxoisovalerate (PubMed:12095615).<ref>PMID:12095615</ref> <ref>PMID:19996101</ref> <ref>PMID:9868782</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/a9/3a9i_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=3a9i ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Homocitrate synthase (HCS) catalyzes aldol-type condensation of acetyl coenzyme A (acetyl-CoA) and alpha-ketoglutarate (alpha-KG) to synthesize homocitrate (HC), which is the first and committed step in the lysine biosynthetic pathway through alpha-aminoadipate. As known in most enzymes catalyzing the first reactions in amino acid biosynthetic pathways, HCS is regulated via feedback inhibition by the end product, lysine. Here, we determined the crystal structures of HCS from Thermus thermophilus complexed with alpha-KG, HC, or lysine. In the HC complex, the C1-carboxyl group of HC, which is derived from acetyl-CoA, is hydrogen-bonded with His-292* from another subunit (indicated by the asterisk), indicating direct involvement of this residue in the catalytic mechanism of HCS. The crystal structure of HCS complexed with lysine showed that lysine is bound to the active site with rearrangement of amino acid residues in the substrate-binding site, which accounts for the competitive inhibition by lysine with alpha-KG. Comparison between the structures suggests that His-72, which is conserved in lysine-sensitive HCSs and binds the C5-carboxyl group of alpha-KG, serves as a switch for the conformational change. Replacement of His-72 by leucine made HCS resistant to lysine inhibition, demonstrating the regulatory role of this conserved residue.
-===Crystal structure of homocitrate synthase from Thermus thermophilus complexed with Lys===
+Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus.,Okada T, Tomita T, Wulandari AP, Kuzuyama T, Nishiyama M J Biol Chem. 2010 Feb 5;285(6):4195-205. Epub 2009 Dec 7. PMID:19996101<ref>PMID:19996101</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3a9i" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19996101}}, adds the Publication Abstract to the page
+*[[Homocitrate synthase|Homocitrate synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19996101 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19996101}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-A9I is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb27 Thermus thermophilus hb27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A9I OCA].
+[[Category: Thermus thermophilus HB27]]
+[[Category: Kuzuyama T]]
-==Reference==
+[[Category: Nishiyama M]]
-<ref group="xtra">PMID:19996101</ref><references group="xtra"/>
+[[Category: Okada T]]
-[[Category: Homocitrate synthase]]
+[[Category: Tomita T]]
-[[Category: Thermus thermophilus hb27]]
-[[Category: Kuzuyama, T.]]
-[[Category: Nishiyama, M.]]
-[[Category: Okada, T.]]
-[[Category: Tomita, T.]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Cytoplasm]]
-[[Category: Homocitrate synthase]]
-[[Category: Lysine biosynthesis]]
-[[Category: Lysine complex]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Dec 24 07:38:05 2009''