2bx7

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,5-dihydroxybenzoate

Structural highlights

2bx7 is a 2 chain structure with sequence from Lactococcus lactis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.04Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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) catalyze the oxidation of dihydroorotate to orotate in the only redox reaction in pyrimidine biosynthesis. The pyrimidine binding sites are very similar in all structurally characterized DHODs, suggesting that the prospects for identifying a class-specific inhibitor directed against this site are poor. Nonetheless, two compounds that bind specifically to the Class 1A DHOD from Lactococcus lactis, 3,4-dihydroxybenzoate (3,4-diOHB) and 3,5-dihydroxybenzoate (3,5-diOHB), have been identified [Palfey et al. (2001) J. Med. Chem. 44, 2861-2864]. The mechanism of inhibitor binding to the Class 1A DHOD from L. lactis has now been studied in detail and is reported here. Titrations showed that 3,4-diOHB binds more tightly at higher pH, whereas the opposite is true for 3,5-diOHB. Isothermal titration calorimetry and absorbance spectroscopy showed that 3,4-diOHB ionizes to the phenolate upon binding to the enzyme, but 3,5-diOHB does not. The charge-transfer band that forms in the 3,4-diOHB complex allowed the kinetics of binding to be observed in stopped-flow experiments. Binding was slow enough to observe from pH 6 to pH 8 and was (minimally) a two-step process consisting of the rapid formation of a complex that isomerized to the final charge-transfer complex. Orotate and 3,5-diOHB bind too quickly to follow directly, but their dissociation kinetics were studied by competition and described adequately with a single step. Crystal structures of both inhibitor complexes were determined, showing that 3,5-diOHB binds in the same orientation as orotate. In contrast, 3,4-diOHB binds in a twisted orientation, enabling one of its phenolic oxygens to form a very strong hydrogen bond to an asparagine, thus stabilizing the phenolate and causing charge-transfer interactions with the pi-system of the flavin, resulting in a green color.

Interaction of benzoate pyrimidine analogues with class 1A dihydroorotate dehydrogenase from Lactococcus lactis.,Wolfe AE, Thymark M, Gattis SG, Fagan RL, Hu YC, Johansson E, Arent S, Larsen S, Palfey BA Biochemistry. 2007 May 15;46(19):5741-53. Epub 2007 Apr 20. PMID:17444658^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Andersen PS, Jansen PJ, Hammer K. Two different dihydroorotate dehydrogenases in Lactococcus lactis. J Bacteriol. 1994 Jul;176(13):3975-82. PMID:8021180
↑ Wolfe AE, Thymark M, Gattis SG, Fagan RL, Hu YC, Johansson E, Arent S, Larsen S, Palfey BA. Interaction of benzoate pyrimidine analogues with class 1A dihydroorotate dehydrogenase from Lactococcus lactis. Biochemistry. 2007 May 15;46(19):5741-53. Epub 2007 Apr 20. PMID:17444658 doi:10.1021/bi7001554

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2bx7"

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF L. LACTIS DIHYDROOROTATE DEHYDROGENSE A IN COMPLEX WITH 3,5-DIHYDROXYBENZOATE==
-<StructureSection load='2bx7' size='340' side='right' caption='[[2bx7]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
+==Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,5-dihydroxybenzoate==
+<StructureSection load='2bx7' size='340' side='right'caption='[[2bx7]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2bx7]] is a 2 chain structure with 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=2BX7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BX7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2bx7]] 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=2BX7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BX7 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=34D:3,5-DIHYDROXYBENZOATE'>34D</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><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]] 2.04&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dor|1dor]], [[1jqv|1jqv]], [[1jqx|1jqx]], [[1jrb|1jrb]], [[1jrc|1jrc]], [[1jub|1jub]], [[1jue|1jue]], [[1nfc|1nfc]], [[1ovd|1ovd]], [[2bsl|2bsl]], [[2dor|2dor]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=34D:3,5-DIHYDROXYBENZOATE'>34D</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</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><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydroorotate_oxidase Dihydroorotate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.1 1.3.3.1] </span></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=2bx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bx7 OCA], [https://pdbe.org/2bx7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bx7 RCSB], [https://www.ebi.ac.uk/pdbsum/2bx7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bx7 ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bx7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bx7 RCSB], [http://www.ebi.ac.uk/pdbsum/2bx7 PDBsum]</span></td></tr>
+</table>
-<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/bx/2bx7_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bx/2bx7_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2bx7 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2bx7" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Dihydroorotate dehydrogenase|Dihydroorotate dehydrogenase]]
+*[[Dihydroorotate dehydrogenase 3D structures|Dihydroorotate dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Dihydroorotate oxidase]]
 [[Category: Lactococcus lactis]]
-[[Category: Arent, S.]]
+[[Category: Large Structures]]
-[[Category: Gattis, S G.]]
+[[Category: Arent S]]
-[[Category: Hansen, M.]]
+[[Category: Gattis SG]]
-[[Category: Hu, Y C.]]
+[[Category: Hansen M]]
-[[Category: Johansson, E.]]
+[[Category: Hu Y-C]]
-[[Category: Larsen, S.]]
+[[Category: Johansson E]]
-[[Category: Palfey, B A.]]
+[[Category: Larsen S]]
-[[Category: Wolfe, A E.]]
+[[Category: Palfey BA]]
-[[Category: Dihydroorotate dehydrogenase]]
+[[Category: Wolfe AE]]
-[[Category: Nucleotide metabolism]]
-[[Category: Oxidoreductase]]

2bx7

From Proteopedia

Current revision

Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,5-dihydroxybenzoate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox