3m5d: Difference between revisions

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-[[Image:3m5d.png|left|200px]]
-<!--
+==Crystal structure of N-acetyl-L-ornithine transcarbamylase K302R mutant complexed with PALAO==
-The line below this paragraph, containing "STRUCTURE_3m5d", creates the "Structure Box" on the page.
+<StructureSection load='3m5d' size='340' side='right'caption='[[3m5d]], [[Resolution|resolution]] 2.20&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'>[[3m5d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M5D 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PA9:N~2~-ACETYL-N~5~-(PHOSPHONOACETYL)-L-ORNITHINE'>PA9</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3m5d|  PDB=3m5d  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3m5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m5d OCA], [https://pdbe.org/3m5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m5d RCSB], [https://www.ebi.ac.uk/pdbsum/3m5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m5d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AOTC_XANCP AOTC_XANCP] Catalyzes the conversion of N-acetylornithine to N-acetylcitrulline in an alternative arginine biosynthesis pathway. The enzyme has no activity with ornithine.
+== 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/m5/3m5d_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=3m5d ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+N-Acetyl-l-ornithine transcarbamylase (AOTCase), rather than ornithine transcarbamylase (OTCase), is the essential carbamylase enzyme in the arginine biosynthesis of several plant and human pathogens. The specificity of this unique enzyme provides a potential target for controlling the spread of these pathogens. Recently, several crystal structures of AOTCase from Xanthomonas campestris (xc) have been determined. In these structures, an unexplained electron density at the tip of the Lys302 side chain was observed. Using (13)C NMR spectroscopy, we show herein that Lys302 is post-translationally carboxylated. The structure of wild-type AOTCase in a complex with the bisubstrate analogue N(delta)-(phosphonoacetyl)-N(alpha)-acetyl-l-ornithine (PALAO) indicates that the carboxyl group on Lys302 forms a strong hydrogen bonding network with surrounding active site residues, Lys252, Ser253, His293, and Glu92 from the adjacent subunit either directly or via a water molecule. Furthermore, the carboxyl group is involved in binding N-acetyl-l-ornithine via a water molecule. Activity assays with the wild-type enzyme and several mutants demonstrate that the post-translational modification of lysine 302 has an important role in catalysis.
-===Crystal structure of N-acetyl-L-ornithine transcarbamylase K302R mutant complexed with PALAO===
+Reversible post-translational carboxylation modulates the enzymatic activity of N-acetyl-L-ornithine transcarbamylase.,Li Y, Yu X, Ho J, Fushman D, Allewell NM, Tuchman M, Shi D Biochemistry. 2010 Aug 17;49(32):6887-95. PMID:20695527<ref>PMID:20695527</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3m5d" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20695527}}, adds the Publication Abstract to the page
+*[[N-acetylornithine carbamoyltransferase|N-acetylornithine carbamoyltransferase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20695527 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20695527}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3m5d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M5D OCA].
-==Reference==
-<ref group="xtra">PMID:20695527</ref><references group="xtra"/>
-[[Category: N-acetylornithine carbamoyltransferase]]
 [[Category: Xanthomonas campestris pv. campestris]]
-[[Category: Allewell, N M.]]
+[[Category: Allewell NM]]
-[[Category: Li, Y.]]
+[[Category: Li Y]]
-[[Category: Shi, D.]]
+[[Category: Shi D]]
-[[Category: Tuchman, M.]]
+[[Category: Tuchman M]]
-[[Category: Yu, X.]]
+[[Category: Yu X]]