2vff: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2vff.png|left|200px]]
-<!--
+==Crystal structure of the F96H mutant of Plasmodium falciparum triosephosphate isomerase==
-The line below this paragraph, containing "STRUCTURE_2vff", creates the "Structure Box" on the page.
+<StructureSection load='2vff' size='340' side='right'caption='[[2vff]], [[Resolution|resolution]] 1.70&Aring;' 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'>[[2vff]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VFF 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]] 1.7&#8491;</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=2vff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vff OCA], [https://pdbe.org/2vff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vff RCSB], [https://www.ebi.ac.uk/pdbsum/2vff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vff ProSAT]</span></td></tr>
-{{STRUCTURE_2vff|  PDB=2vff  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TPIS_PLAFA TPIS_PLAFA]
+== 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/vf/2vff_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=2vff ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The k(cat) values and K(m) values are (2.54 +/- 0.19) x 10(5) min(-1) and 0.39 +/- 0.049 mM, respectively, for the wild type; (3.72 +/- 0.28) x 10(3) min(-1) and 2.18 +/- 0.028 mM, respectively, for the F96S mutant; (1.11 +/- 0.03) x 10(4) min(-1) and 2.62 +/- 0.042 mM, respectively, for the F96H mutant; and (1.48 +/- 0.05) x 10(5) min(-1) and 1.20 +/- 0.056 mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM.
-===CRYSTAL STRUCTURE OF THE F96H MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE===
+Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site.,Gayathri P, Banerjee M, Vijayalakshmi A, Balaram H, Balaram P, Murthy MR Acta Crystallogr D Biol Crystallogr. 2009 Aug;65(Pt 8):847-57. Epub 2009, Jul 17. PMID:19622869<ref>PMID:19622869</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vff" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-VFF is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VFF OCA].
+*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]]
+*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Plasmodium falciparum]]
-[[Category: Triose-phosphate isomerase]]
+[[Category: Balaram H]]
-[[Category: Balaram, H.]]
+[[Category: Balaram P]]
-[[Category: Balaram, P.]]
+[[Category: Banerjee M]]
-[[Category: Banerjee, M.]]
+[[Category: Gayathri P]]
-[[Category: Gayathri, P.]]
+[[Category: Murthy MRN]]
-[[Category: Murthy, M R.N.]]
+[[Category: Vijayalakshmi A]]
-[[Category: Vijayalakshmi, A.]]
-[[Category: Fatty acid biosynthesis]]
-[[Category: Gluconeogenesis]]
-[[Category: Glycolysis]]
-[[Category: Isomerase]]
-[[Category: Lipid synthesis]]
-[[Category: Loop open]]
-[[Category: Mutant]]
-[[Category: Pentose shunt]]
-[[Category: Plasmodium falciparum]]
-[[Category: Tim]]
-[[Category: Triosephosphate isomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug  5 20:35:01 2009''