6cty: Difference between revisions
New page: ==Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution== <StructureSection load='6cty' size='340' side='right' caption='[[6cty... |
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==Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution== | ==Crystal structure of dihydroorotase pyrC from Yersinia pestis in complex with zinc and malate at 2.4 A resolution== | ||
<StructureSection load='6cty' size='340' side='right' caption='[[6cty]], [[Resolution|resolution]] 2.41Å' scene=''> | <StructureSection load='6cty' size='340' side='right'caption='[[6cty]], [[Resolution|resolution]] 2.41Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6cty]] is a 6 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5v0g 5v0g]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CTY OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6cty]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5v0g 5v0g]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CTY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CTY FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.41Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MLT:D-MALATE'>MLT</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=6cty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cty OCA], [https://pdbe.org/6cty PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cty RCSB], [https://www.ebi.ac.uk/pdbsum/6cty PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cty ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/PYRC_YERPE PYRC_YERPE] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The de novo pyrimidine biosynthesis pathway is essential for the proliferation of many pathogens. One of the pathway enzymes, dihydroorotase (DHO), catalyzes the reversible interconversion of N-carbamoyl-l-aspartate to 4,5-dihydroorotate. The substantial difference between bacterial and mammalian DHOs makes it a promising drug target for disrupting bacterial growth and thus an important candidate to evaluate as a response to antimicrobial resistance on a molecular level. Here, we present two novel three-dimensional structures of DHOs from Yersinia pestis (YpDHO), the plague-causing pathogen, and Vibrio cholerae (VcDHO), the causative agent of cholera. The evaluations of these two structures led to an analysis of all available DHO structures and their classification into known DHO types. Comparison of all the DHO active sites containing ligands that are listed in DrugBank was facilitated by a new interactive, structure-comparison and presentation platform. In addition, we examined the genetic context of characterized DHOs, which revealed characteristic patterns for different types of DHOs. We also generated a homology model for DHO from Plasmodium falciparum. | |||
Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.,Lipowska J, Miks CD, Kwon K, Shuvalova L, Zheng H, Lewinski K, Cooper DR, Shabalin IG, Minor W Int J Biol Macromol. 2019 Sep 1;136:1176-1187. doi:, 10.1016/j.ijbiomac.2019.05.149. Epub 2019 Jun 15. PMID:31207330<ref>PMID:31207330</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6cty" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Dihydroorotase 3D structures|Dihydroorotase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Yersinia pestis]] | ||
[[Category: | [[Category: Anderson WF]] | ||
[[Category: Cooper | [[Category: Cooper DR]] | ||
[[Category: Kwon | [[Category: Kwon K]] | ||
[[Category: Lipowska | [[Category: Lipowska J]] | ||
[[Category: Minor | [[Category: Minor W]] | ||
[[Category: Shabalin | [[Category: Shabalin IG]] | ||
[[Category: Shuvalova | [[Category: Shuvalova L]] | ||
[[Category: Winsor | [[Category: Winsor J]] | ||
[[Category: Woinska | [[Category: Woinska M]] | ||