4lcr: Difference between revisions
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The | ==The crystal structure of di-Zn dihydropyrimidinase in complex with NCBA== | ||
<StructureSection load='4lcr' size='340' side='right'caption='[[4lcr]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4lcr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Tetraodon_nigroviridis Tetraodon nigroviridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LCR FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=URP:N-(AMINOCARBONYL)-BETA-ALANINE'>URP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4lcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lcr OCA], [https://pdbe.org/4lcr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lcr RCSB], [https://www.ebi.ac.uk/pdbsum/4lcr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lcr ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q4SMR4_TETNG Q4SMR4_TETNG] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Lysine carbamylation, a post-translational modification, facilitates metal coordination for specific enzymatic activities. We have determined structures of the vertebrate dihydropyrimidinase from Tetraodon nigroviridis (TnDhp) in various states: the apo enzyme as well as two forms of the holo enzyme with one and two metals at the catalytic site. The essential active-site structural requirements have been identified with possible existence of four metal-mediated stages of lysine carbamylation. Only one metal is sufficient for stabilizing lysine carbamylation; however, the post-translational lysine carbamylation facilitates additional metal coordination for the regulation of specific enzymatic activities through controlling the conformations of two dynamic loops, Ala69-Arg74 and Met158-Met165, located in the tunnel for the substrate entrance. The substrate/product tunnel is in the ''open form'' in the apo-TnDhp, in the ''intermediate state'' in the mono-metal TnDhp, and in the ''close form'' in the di-metal TnDhp structure, respectively. Structural comparison also suggests that the C-terminal tail plays a role in the enzymatic function through interactions with the Ala69-Arg74 dynamic loop. In addition, the structures of the di-metal TnDhp in complexes with hydantoin, N-carbomyl-beta-alanine and N-carbomyl-beta-aminoisobutyrate, as well as apo-TnDhp in complex with a product analog, N-(2-acetamido)-iminodiacetic acid, have been determined. These structural results illustrate how a protein exploits unique lysines and the metal distribution to accomplish lysine carbamylation as well as subsequent enzymatic functions. | |||
Crystal Structures of Vertebrate Dihydropyrimidinase and Complexes from Tetraodon Nigroviridis with Lysine Carbamylation: Metal and Structural Requirements for Post-Translational Modification and Function.,Hsieh YC, Chen MC, Hsu CC, Chan SI, Yang YS, Chen CJ J Biol Chem. 2013 Sep 4. PMID:24005677<ref>PMID:24005677</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4lcr" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Tetraodon nigroviridis]] | |||
[[Category: Chan SI]] | |||
[[Category: Chen CJ]] | |||
[[Category: Chen MC]] | |||
[[Category: Hsieh YC]] | |||
[[Category: Hsu CC]] | |||
[[Category: Yang YS]] | |||