2blb: Difference between revisions

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-[[Image:2blb.gif|left|200px]]
- {{Structure
+==X-ray crystal structure of Plasmodium vivax dihydrofolate reductase in complex with pyrimethamine and its derivative==
-|PDB= 2blb |SIZE=350|CAPTION= <scene name='initialview01'>2blb</scene>, resolution 3.00&Aring;
+<StructureSection load='2blb' size='340' side='right'caption='[[2blb]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Mes+Binding+Site+For+Chain+A'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=CP7:6-ETHYL-5-PHENYLPYRIMIDINE-2,4-DIAMINE'>CP7</scene> and <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC ACID'>MES</scene>
+<table><tr><td colspan='2'>[[2blb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BLB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BLB FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CP7:6-ETHYL-5-PHENYLPYRIMIDINE-2,4-DIAMINE'>CP7</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=2blb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2blb OCA], [https://pdbe.org/2blb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2blb RCSB], [https://www.ebi.ac.uk/pdbsum/2blb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2blb ProSAT], [https://www.topsan.org/Proteins/RSGI/2blb TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DRTS_PLAVI DRTS_PLAVI] Bifunctional enzyme. Involved in de novo dTMP biosynthesis. Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, DNA precursor synthesis, and for the conversion of dUMP to dTMP.
+== 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/bl/2blb_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=2blb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pyrimethamine (Pyr) targets dihydrofolate reductase of Plasmodium vivax (PvDHFR) as well as other malarial parasites, but its use as antimalarial is hampered by the widespread high resistance. Comparison of the crystal structures of PvDHFR from wild-type and the Pyr-resistant (SP21, Ser-58 --&gt; Arg + Ser-117 --&gt; Asn) strain as complexes with NADPH and Pyr or its analog lacking p-Cl (Pyr20) clearly shows that the steric conflict arising from the side chain of Asn-117 in the mutant enzyme, accompanied by the loss of binding to Ser-120, is mainly responsible for the reduction in binding of Pyr. Pyr20 still effectively inhibits both the wild-type and SP21 proteins, and the x-ray structures of these complexes show how Pyr20 fits into both active sites without steric strain. These structural insights suggest a general approach for developing new generations of antimalarial DHFR inhibitors that, by only occupying substrate space of the active site, would retain binding affinity with the mutant enzymes.
-'''X-RAY CRYSTAL STRUCTURE OF PLASMODIUM VIVAX DIHYDROFOLATE REDUCTASE IN COMPLEX WITH PYRIMETHAMINE AND ITS DERIVATIVE'''
+Crystal structure of dihydrofolate reductase from Plasmodium vivax: pyrimethamine displacement linked with mutation-induced resistance.,Kongsaeree P, Khongsuk P, Leartsakulpanich U, Chitnumsub P, Tarnchompoo B, Walkinshaw MD, Yuthavong Y Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13046-51. Epub 2005 Aug 31. PMID:16135570<ref>PMID:16135570</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2blb" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Pyrimethamine (Pyr) targets dihydrofolate reductase of Plasmodium vivax (PvDHFR) as well as other malarial parasites, but its use as antimalarial is hampered by the widespread high resistance. Comparison of the crystal structures of PvDHFR from wild-type and the Pyr-resistant (SP21, Ser-58 --&gt; Arg + Ser-117 --&gt; Asn) strain as complexes with NADPH and Pyr or its analog lacking p-Cl (Pyr20) clearly shows that the steric conflict arising from the side chain of Asn-117 in the mutant enzyme, accompanied by the loss of binding to Ser-120, is mainly responsible for the reduction in binding of Pyr. Pyr20 still effectively inhibits both the wild-type and SP21 proteins, and the x-ray structures of these complexes show how Pyr20 fits into both active sites without steric strain. These structural insights suggest a general approach for developing new generations of antimalarial DHFR inhibitors that, by only occupying substrate space of the active site, would retain binding affinity with the mutant enzymes.
+*[[Dihydrofolate reductase 3D structures|Dihydrofolate reductase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-BLB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BLB OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Crystal structure of dihydrofolate reductase from Plasmodium vivax: pyrimethamine displacement linked with mutation-induced resistance., Kongsaeree P, Khongsuk P, Leartsakulpanich U, Chitnumsub P, Tarnchompoo B, Walkinshaw MD, Yuthavong Y, Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13046-51. Epub 2005 Aug 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16135570 16135570]
-[[Category: Dihydrofolate reductase]]
 [[Category: Plasmodium vivax]]
-[[Category: Single protein]]
+[[Category: Chitnumsub P]]
-[[Category: Chitnumsub, P.]]
+[[Category: Khongsuk P]]
-[[Category: Khongsuk, P.]]
+[[Category: Kongsaeree P]]
-[[Category: Kongsaeree, P.]]
+[[Category: Leartsakulpanich U]]
-[[Category: Leartsakulpanich, U.]]
+[[Category: Tarnchompoo B]]
-[[Category: Tarnchompoo, B.]]
+[[Category: Walkinshaw MD]]
-[[Category: Walkinshaw, M D.]]
+[[Category: Yuthavong Y]]
-[[Category: Yuthavong, Y.]]
-[[Category: CP7]]
-[[Category: MES]]
-[[Category: NDP]]
-[[Category: dihydrofolate reductase]]
-[[Category: drug resistance]]
-[[Category: malaria]]
-[[Category: oxidoreductase]]
-[[Category: plamodium vivax]]
-[[Category: pyrimethamine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:03:25 2008''