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| | ==1.8 A resolution structure of native lactococcus lactis dihydroorotate dehydrogenase A== | | ==1.8 A resolution structure of native lactococcus lactis dihydroorotate dehydrogenase A== |
| - | <StructureSection load='1jue' size='340' side='right' caption='[[1jue]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='1jue' size='340' side='right'caption='[[1jue]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1jue]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_lactis"_lister_1873 "bacterium lactis" lister 1873]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JUE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JUE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1jue]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JUE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dor|1dor]], [[2dor|2dor]], [[1jqv|1jqv]], [[1jqx|1jqx]], [[1jrb|1jrb]], [[1jrc|1jrc]], [[1jub|1jub]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PyrD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1358 "Bacterium lactis" Lister 1873])</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=1jue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jue OCA], [https://pdbe.org/1jue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jue RCSB], [https://www.ebi.ac.uk/pdbsum/1jue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jue ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotate_oxidase_(fumarate) Dihydroorotate oxidase (fumarate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.98.1 1.3.98.1] </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=1jue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jue OCA], [http://pdbe.org/1jue PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jue RCSB], [http://www.ebi.ac.uk/pdbsum/1jue PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jue ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PYRDA_LACLC PYRDA_LACLC]] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor (By similarity). | + | [https://www.uniprot.org/uniprot/PYRDA_LACLM PYRDA_LACLM] Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro, but cannot use NAD(+) as an electron acceptor.<ref>PMID:8021180</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1jue" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1jue" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Dihydroorotate dehydrogenase 3D structures|Dihydroorotate dehydrogenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacterium lactis lister 1873]] | + | [[Category: Lactococcus lactis]] |
| - | [[Category: Arent, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Bjornberg, O]] | + | [[Category: Arent S]] |
| - | [[Category: Jensen, K F]] | + | [[Category: Bjornberg O]] |
| - | [[Category: Larsen, S]] | + | [[Category: Jensen KF]] |
| - | [[Category: Leggio, L Lo]] | + | [[Category: Larsen S]] |
| - | [[Category: Norager, S]] | + | [[Category: Lo Leggio L]] |
| - | [[Category: Ottosen, M]] | + | [[Category: Norager S]] |
| - | [[Category: Alpha-beta barrel]]
| + | [[Category: Ottosen M]] |
| - | [[Category: Flavoprotein]]
| + | |
| - | [[Category: Homodimer]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
PYRDA_LACLM Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro, but cannot use NAD(+) as an electron acceptor.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Dihydroorotate dehydrogenases (DHODs) are flavoenzymes catalyzing the oxidation of (S)-dihydroorotate to orotate in the biosynthesis of UMP, the precursor of all other pyrimidine nucleotides. On the basis of sequence, DHODs can be divided into two classes, class 1, further divided in subclasses 1A and 1B, and class 2. This division corresponds to differences in cellular location and the nature of the electron acceptor. Herein we report a study of Lactococcus lactis DHODA, a representative of the class 1A enzymes. Based on the DHODA structure we selected seven residues that are highly conserved between both main classes of DHODs as well as three residues representing surface charges close to the active site for site-directed mutagenesis. The availability of both kinetic and structural data on the mutant enzymes allowed us to define the roles individual structural segments play in catalysis. We have also structurally proven the presence of an open active site loop in DHODA and obtained information about the interactions that control movements of loops around the active site. Furthermore, in one mutant structure we observed differences between the two monomers of the dimer, confirming an apparent asymmetry between the two substrate binding sites that was indicated by the kinetic results.
Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function.,Norager S, Arent S, Bjornberg O, Ottosen M, Lo Leggio L, Jensen KF, Larsen S J Biol Chem. 2003 Aug 1;278(31):28812-22. Epub 2003 May 5. PMID:12732650[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Andersen PS, Jansen PJ, Hammer K. Two different dihydroorotate dehydrogenases in Lactococcus lactis. J Bacteriol. 1994 Jul;176(13):3975-82. PMID:8021180
- ↑ Norager S, Arent S, Bjornberg O, Ottosen M, Lo Leggio L, Jensen KF, Larsen S. Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function. J Biol Chem. 2003 Aug 1;278(31):28812-22. Epub 2003 May 5. PMID:12732650 doi:10.1074/jbc.M303767200
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