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| | ==Hybrid dihydroorotase domain of human CAD with E. coli flexible loop, bound to dihydroorotate== | | ==Hybrid dihydroorotase domain of human CAD with E. coli flexible loop, bound to dihydroorotate== |
| - | <StructureSection load='6hg3' size='340' side='right' caption='[[6hg3]], [[Resolution|resolution]] 1.97Å' scene=''> | + | <StructureSection load='6hg3' size='340' side='right'caption='[[6hg3]], [[Resolution|resolution]] 1.97Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6hg3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HG3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HG3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6hg3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HG3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HG3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOR:(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>DOR</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.97Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOR:(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC+ACID'>DOR</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CAD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6hg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hg3 OCA], [https://pdbe.org/6hg3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hg3 RCSB], [https://www.ebi.ac.uk/pdbsum/6hg3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hg3 ProSAT]</span></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=6hg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hg3 OCA], [http://pdbe.org/6hg3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hg3 RCSB], [http://www.ebi.ac.uk/pdbsum/6hg3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hg3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PYR1_HUMAN PYR1_HUMAN]] This protein is a "fusion" protein encoding four enzymatic activities of the pyrimidine pathway (GATase, CPSase, ATCase and DHOase). | + | [https://www.uniprot.org/uniprot/PYR1_HUMAN PYR1_HUMAN] This protein is a "fusion" protein encoding four enzymatic activities of the pyrimidine pathway (GATase, CPSase, ATCase and DHOase). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6hg3" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6hg3" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[CAD protein|CAD protein]] |
| | + | *[[CAD protein 3D structures|CAD protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Cano-Ochoa, F Del]] | + | [[Category: Large Structures]] |
| - | [[Category: Ramon-Maiques, S]] | + | [[Category: Del Cano-Ochoa F]] |
| - | [[Category: Biosynthetic protein]] | + | [[Category: Ramon-Maiques S]] |
| - | [[Category: Cad]]
| + | |
| - | [[Category: Carboxylated lysine]]
| + | |
| - | [[Category: De novo pyrimidine biosynthesis]]
| + | |
| - | [[Category: Tim-barrel]]
| + | |
| Structural highlights
Function
PYR1_HUMAN This protein is a "fusion" protein encoding four enzymatic activities of the pyrimidine pathway (GATase, CPSase, ATCase and DHOase).
Publication Abstract from PubMed
The dihydroorotase (DHOase) domain of the multifunctional protein carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase (CAD) catalyzes the third step in the de novo biosynthesis of pyrimidine nucleotides in animals. The crystal structure of the DHOase domain of human CAD (huDHOase) revealed that, despite evolutionary divergence, its active site components are highly conserved with those in bacterial DHOases, encoded as monofunctional enzymes. An important element for catalysis, conserved from Escherichia coli to humans, is a flexible loop that closes as a lid over the active site. Here, we combined mutagenic, structural, biochemical, and molecular dynamics analyses to characterize the function of the flexible loop in the activity of CAD's DHOase domain. A huDHOase chimera bearing the E. coli DHOase flexible loop was inactive, suggesting the presence of distinctive elements in the flexible loop of huDHOase that cannot be replaced by the bacterial sequence. We pinpoint Phe-1563, a residue absolutely conserved at the tip of the flexible loop in CAD's DHOase domain, as a critical element for the conformational equilibrium between the two catalytic states of the protein. Substitutions of Phe-1563 with Ala, Leu or Thr prevented the closure of the flexible loop and inactivated the protein, whereas substitution with Tyr enhanced the interactions of the loop in the closed position and reduced fluctuations and the reaction rate. Our results confirm the importance of the flexible loop in CAD's DHOase domain and explain the key role of Phe-1563 in configuring the active site and in promoting substrate strain and catalysis.
Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD.,Del Cano-Ochoa F, Grande-Garcia A, Reverte-Lopez M, D'Abramo M, Ramon-Maiques S J Biol Chem. 2018 Oct 12. pii: RA118.005494. doi: 10.1074/jbc.RA118.005494. PMID:30315107[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Del Cano-Ochoa F, Grande-Garcia A, Reverte-Lopez M, D'Abramo M, Ramon-Maiques S. Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD. J Biol Chem. 2018 Oct 12. pii: RA118.005494. doi: 10.1074/jbc.RA118.005494. PMID:30315107 doi:http://dx.doi.org/10.1074/jbc.RA118.005494
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