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| - | [[Image:1dor.gif|left|200px]] | |
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| - | <!-- | + | ==DIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS== |
| - | The line below this paragraph, containing "STRUCTURE_1dor", creates the "Structure Box" on the page.
| + | <StructureSection load='1dor' size='340' side='right'caption='[[1dor]], [[Resolution|resolution]] 2.00Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1dor]] 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=1DOR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DOR FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
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| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr> |
| - | {{STRUCTURE_1dor| PDB=1dor | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dor FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dor OCA], [https://pdbe.org/1dor PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dor RCSB], [https://www.ebi.ac.uk/pdbsum/1dor PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dor ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [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 == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/do/1dor_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dor ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''DIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS'''
| + | ==See Also== |
| - | | + | *[[Dihydroorotate dehydrogenase 3D structures|Dihydroorotate dehydrogenase 3D structures]] |
| - | | + | == References == |
| - | ==Overview== | + | <references/> |
| - | BACKGROUND:. Dihydroorotate dehydrogenase (DHOD) is a flavin mononucleotide containing enzyme, which catalyzes the oxidation of (S)-dihydroorotate to orotate, the fourth step in the de novo biosynthesis of pyrimidine nucleotides. Lactococcus lactis contains two genes encoding different functional DHODs whose sequences are only 30% identical. One of these enzymes, DHODA, is a highly efficient dimer, while the other, DHODB, shows optimal activity only in the presence of an iron-sulphur cluster containing protein with which it forms a complex tetramer. Sequence alignments have identified three different families among the DHODs: the two L. lactis enzymes belong to two of the families, whereas the enzyme from E. coli is a representative of the third. As no three-dimensional structures of DHODs are currently available, we set out to determine the crystal structure of DHODA from L. lactis. The differences between the two L. lactis enzymes make them particularly interesting for studying flavoprotein redox reactions and for identifying the differences between the enzyme families. RESULTS:. The crystal structure of DHODA has been determined to 2.0 resolution. The enzyme is a dimer of two crystallographically independent molecules related by a non-crystallographic twofold axis. The protein folds into and alpha/beta barrel with the flavin molecule sitting between the top of the barrel and a subdomain formed by several barrel inserts. Above the flavin isoalloxazine ring there is a small water filled cavity, completely buried beneath the protein surface and surrounded by many conserved residues. This cavity is proposed as the substrate-binding site. CONCLUSIONS:. The crystal structure has allowed the function of many of the conserved residues in DHODs to be identified: many of these are associated with binding the flavin group. Important differences were identified in some of the active-site residues which vary across the distinct DHOD families, implying significant mechanistic differences. The substrate cavity, although buried, is located beneath a highly conserved loop which is much less ordered than the rest of the protein and may be important in giving access to the cavity. The location of the conserved residues surrounding this cavity suggests the potential orientation of the substrate.
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==About this Structure== | + | |
| - | 1DOR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DOR OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis., Rowland P, Nielsen FS, Jensen KF, Larsen S, Structure. 1997 Feb 15;5(2):239-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9032071 9032071]
| + | |
| - | [[Category: Dihydroorotate oxidase]]
| + | |
| | [[Category: Lactococcus lactis]] | | [[Category: Lactococcus lactis]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Larsen, S.]] | + | [[Category: Larsen S]] |
| - | [[Category: Rowland, P.]] | + | [[Category: Rowland P]] |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Pyrimidine nucleotide biosynthesis]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 14:05:41 2008''
| + | |
