1ay8: Difference between revisions

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-{{Seed}}
-[[Image:1ay8.png|left|200px]]
-<!--
+==AROMATIC AMINO ACID AMINOTRANSFERASE COMPLEX WITH 3-PHENYLPROPIONATE==
-The line below this paragraph, containing "STRUCTURE_1ay8", creates the "Structure Box" on the page.
+<StructureSection load='1ay8' size='340' side='right'caption='[[1ay8]], [[Resolution|resolution]] 2.30&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'>[[1ay8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AY8 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HCI:HYDROCINNAMIC+ACID'>HCI</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-{{STRUCTURE_1ay8|  PDB=1ay8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ay8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ay8 OCA], [https://pdbe.org/1ay8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ay8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ay8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ay8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TYRB_PARDE TYRB_PARDE] Shows activities toward both dicarboxylic and aromatic substrates.
+== 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/ay/1ay8_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=1ay8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Aminotransferase reversibly catalyzes the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5'-phosphate (PLP) as a cofactor. Various kinds of aminotransferases developing into catalysts for particular substrates have been reported. Among the aminotransferases, aromatic amino acid aminotransferase (EC 2.6.1. 57) catalyzes the transamination reaction with both acidic substrates and aromatic substrates. To elucidate the multiple substrate recognition mechanism, we determined the crystal structures of aromatic amino acid aminotransferase from Paracoccus denitrificans (pdAroAT): unliganded pdAroAT, pdAroAT in a complex with maleate as an acidic substrate analog, and pdAroAT in a complex with 3-phenylpropionate as an aromatic substrate analog at 2.33 A, 2. 50 A and 2.30 A resolution, respectively. The pdAroAT molecule is a homo-dimer. Each subunit has 394 amino acids and one PLP and is divided into small and large domains. The overall structure of pdAroAT is essentially identical to that of aspartate aminotransferase (AspAT) which catalyzes the transamination reaction with only an acidic amino acid. On binding the acidic substrate analog, arginine 292 and 386 form end-on salt bridges with carboxylates of the analog. Furthermore, binding of the substrate induces the domain movement to close the active site. The recognition mechanism for the acidic substrate analog in pdAroAT is identical to that observed in AspAT. Binding of the aromatic substrate analog causes reorientation of the side-chain of the residues, lysine 16, asparagine 142, arginine 292* and serine 296*, and changes in the position of water molecules in the active site to form a new hydrogen bond network in contrast to the active site structure of pdAroAT in the complex with an acidic substrate analog. Consequently, the rearrangement of the hydrogen bond network can form recognition sites for both acidic and aromatic side-chains of the substrate without a conformational change in the backbone structure in pdAroAT.
-===AROMATIC AMINO ACID AMINOTRANSFERASE COMPLEX WITH 3-PHENYLPROPIONATE===
+Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network.,Okamoto A, Nakai Y, Hayashi H, Hirotsu K, Kagamiyama H J Mol Biol. 1998 Jul 17;280(3):443-61. PMID:9665848<ref>PMID:9665848</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ay8" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9665848}}, adds the Publication Abstract to the page
+*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9665848 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9665848}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-AY8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AY8 OCA].
-==Reference==
-Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network., Okamoto A, Nakai Y, Hayashi H, Hirotsu K, Kagamiyama H, J Mol Biol. 1998 Jul 17;280(3):443-61. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9665848 9665848]
-[[Category: Aromatic-amino-acid transaminase]]
 [[Category: Paracoccus denitrificans]]
-[[Category: Single protein]]
+[[Category: Hirotsu K]]
-[[Category: Hirotsu, K.]]
+[[Category: Kagamiyama H]]
-[[Category: Kagamiyama, H.]]
+[[Category: Okamoto A]]
-[[Category: Okamoto, A.]]
-[[Category: Aminotransferase]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 17:50:45 2008''