3cbf: Difference between revisions

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-[[Image:3cbf.png|left|200px]]
-<!--
+==Crystal structure of LysN, alpha-aminoadipate aminotransferase, from Thermus thermophilus HB27==
-The line below this paragraph, containing "STRUCTURE_3cbf", creates the "Structure Box" on the page.
+<StructureSection load='3cbf' size='340' side='right'caption='[[3cbf]], [[Resolution|resolution]] 1.67&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'>[[3cbf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CBF 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]] 1.67&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N5F:(2S)-2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]HEXANEDIOIC+ACID'>N5F</scene></td></tr>
-{{STRUCTURE_3cbf|  PDB=3cbf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cbf OCA], [https://pdbe.org/3cbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cbf RCSB], [https://www.ebi.ac.uk/pdbsum/3cbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cbf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LYSN_THET2 LYSN_THET2] Catalyzes the transfer of an amino group between 2-oxoadipate (2-OA) and glutamate (Glu) to yield alpha-aminodipate (AAA). It can also transaminate glutamate, leucine, and aromatic amino acids. It also contributes in the biosynthesis of other amino acids such as leucine.<ref>PMID:15256574</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/cb/3cbf_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=3cbf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+alpha-Aminoadipate aminotransferase (AAA-AT), a homolog of mammalian kynurenine aminotransferase II (Kat II), transfers an amino group to 2-oxoadipate to yield alpha-aminoadipate in lysine biosynthesis through the alpha-aminoadipate pathway in Thermus thermophilus. AAA-AT catalyzes transamination against various substrates, including AAA, glutamate, leucine, and aromatic amino acids. To elucidate the structural change for recognition of various substrates, we determined crystal structures of AAA-AT in four forms: with pyridoxal 5'-phosphate (PLP) (PLP complex), with PLP and leucine (PLP/Leu complex), with N-phosphopyridoxyl-leucine (PPL) (PPL complex), and with N-phosphopyridoxyl-alpha-aminoadipate (PPA) at 2.67, 2.26, 1.75, and 1.67 A resolution, respectively. The PLP complex is in an open state, whereas PLP/Leu, PPL, and PPA complexes are in closed states with maximal displacement (over 7 A) of the alpha2 helix and the beta1 strand in the small domain to cover the active site, indicating that conformational change is induced by substrate binding. In PPL and PLP/Leu complexes, several hydrophobic residues on the alpha2 helix recognize the hydrophobic side chain of the bound leucine moiety whereas, in the PPA complex, the alpha2 helix rotates to place the guanidium moiety of Arg23 on the helix at the appropriate position to interact with the carboxyl side chain of the AAA moiety. These results indicate that AAA-AT can recognize various kinds of substrates using the mobile alpha2 helix. The crystal structures and site-directed mutagenesis revealed that intersubunit-electrostatic interactions contribute to the elevated thermostability of this enzyme. Proteins 2008. (c) 2008 Wiley-Liss, Inc.
-===Crystal structure of LysN, alpha-aminoadipate aminotransferase, from Thermus thermophilus HB27===
+Mechanism for multiple-substrates recognition of alpha-aminoadipate aminotransferase from Thermus thermophilus.,Tomita T, Miyagawa T, Miyazaki T, Fushinobu S, Kuzuyama T, Nishiyama M Proteins. 2008 Sep 2. PMID:18831049<ref>PMID:18831049</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3cbf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18831049}}, adds the Publication Abstract to the page
+*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18831049 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18831049}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3cbf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CBF OCA].
-==Reference==
-<ref group="xtra">PMID:18831049</ref><ref group="xtra">PMID:15256574</ref><references group="xtra"/>
-[[Category: 2-aminoadipate transaminase]]
-[[Category: Thermus thermophilus]]
-[[Category: Fushinobu, S.]]
-[[Category: Kuzuyama, T.]]
-[[Category: Miyagawa, T.]]
-[[Category: Miyazaki, T.]]
-[[Category: Nishiyama, M.]]
-[[Category: Tomita, T.]]
-[[Category: Alpha-aminoadipate aminotransferase]]
-[[Category: Substrate specifity]]
 [[Category: Thermus thermophilus]]
+[[Category: Fushinobu S]]
+[[Category: Kuzuyama T]]
+[[Category: Miyagawa T]]
+[[Category: Miyazaki T]]
+[[Category: Nishiyama M]]
+[[Category: Tomita T]]