3daa: Difference between revisions

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 ==CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE==
-<StructureSection load='3daa' size='340' side='right' caption='[[3daa]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='3daa' size='340' side='right'caption='[[3daa]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3daa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DAA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3daa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._YM-1 Bacillus sp. YM-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DAA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa PDBsum]</span></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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [https://pdbe.org/3daa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [https://www.ebi.ac.uk/pdbsum/3daa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3daa ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DAAA_BACYM DAAA_BACYM] Acts on the D-isomers of alanine, leucine, aspartate, glutamate, aminobutyrate, norvaline and asparagine. The enzyme transfers an amino group from a substrate D-amino acid to the pyridoxal phosphate cofactor to form pyridoxamine and an alpha-keto acid in the first half-reaction. The second-half reaction is the reverse of the first, transferring the amino group from the pyridoxamine to a second alpha-keto acid to form the product D-amino acid via a ping-pong mechanism. This is an important process in the formation of D-alanine and D-glutamate, which are essential bacterial cell wall components.<ref>PMID:2914916</ref> <ref>PMID:9538014</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/da/3daa_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/3daa_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3daa ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3daa" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
+*[[Aspartate aminotransferase 3D structures|Aspartate aminotransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus sp]]
+[[Category: Bacillus sp. YM-1]]
-[[Category: D-amino-acid transaminase]]
+[[Category: Large Structures]]
-[[Category: Chipman, D M]]
+[[Category: Chipman DM]]
-[[Category: Peisach, D]]
+[[Category: Peisach D]]
-[[Category: Ringe, D]]
+[[Category: Ringe D]]
-[[Category: Aminotransferase]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Transaminase]]