View source for 9yd7


==Complex of Dihydroorotase from M. jannaschii with Carbamoyl Aspartate==
<StructureSection load='9yd7' size='340' side='right'caption='[[9yd7]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9yd7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9YD7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9YD7 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.87&#8491;</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=NCD:N-CARBAMOYL-L-ASPARTATE'>NCD</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=9yd7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9yd7 OCA], [https://pdbe.org/9yd7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9yd7 RCSB], [https://www.ebi.ac.uk/pdbsum/9yd7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9yd7 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PYRC_METJA PYRC_METJA] Catalyzes the reversible cyclization of carbamoyl aspartate to dihydroorotate.[HAMAP-Rule:MF_00220]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Here, we report the X-ray structural analysis of dihydroorotase from Methanococcus jannaschii co-crystallized with dihydroorotate at pH 6.5. The crystals are isomorphous with the crystals of the apoenzyme, with space group P3(2)21 and unit-cell dimensions a = b = 111.4, c = 101.2 A. The structure was refined to R = 0.169 and R(free) = 0.186 at a resolution of 1.87 A at room temperature. During crystallization the degradative reaction took place, and the electron density in the active site corresponds to the substrate carbamoyl aspartate. Carbamoyl aspartate interacts with the protein in the active site in a manner similar to that observed for Escherichia coli and human dihydroorotases. However, the flexible loop (residues 140-151) adopts both conformations in the crystal, loop-out and loop-in, with the loop-out conformation having higher occupancy. This contrasts with our expectations for the flexible loop to be exclusively in the loop-in conformation, which is the conformation that it adopts to stabilize the binding of the substrate in the known systems. Additional studies with substrate analogs that resemble carbamoyl aspartate and different crystallization conditions would provide further insight into the conformation of the flexible loop in this system.

Crystal structure of Methanococcus jannaschii dihydroorotase with substrate bound.,Vitali J, Nix JC, Newman HE, Colaneri MJ Acta Crystallogr F Struct Biol Commun. 2026 Jan 1. doi: , 10.1107/S2053230X25010556. PMID:41355244<ref>PMID:41355244</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9yd7" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Colaneri MJ]]
[[Category: Newman HE]]
[[Category: Nix JC]]
[[Category: Vitali J]]