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| - | [[Image:1f4p.gif|left|200px]] | |
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| - | <!-- | + | ==Y98W FLAVODOXIN MUTANT 1.5A (D. VULGARIS)== |
| - | The line below this paragraph, containing "STRUCTURE_1f4p", creates the "Structure Box" on the page.
| + | <StructureSection load='1f4p' size='340' side='right'caption='[[1f4p]], [[Resolution|resolution]] 1.30Å' 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'>[[1f4p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F4P 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]] 1.3Å</td></tr> |
| - | --> | + | <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_1f4p| PDB=1f4p | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f4p OCA], [https://pdbe.org/1f4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f4p RCSB], [https://www.ebi.ac.uk/pdbsum/1f4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f4p ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/FLAV_DESVH FLAV_DESVH] Low-potential electron donor to a number of redox enzymes. |
| | + | == 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/f4/1f4p_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=1f4p ConSurf]. |
| | + | <div style="clear:both"></div> |
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| - | '''Y98W FLAVODOXIN MUTANT 1.5A (D. VULGARIS)'''
| + | ==See Also== |
| - | | + | *[[Flavodoxin 3D structures|Flavodoxin 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | The structures for two mutants at the Tyr98 site of Desulfovibrio vulgaris flavodoxin have been determined. The first, a tyrosine-to-histidine (Y98H) variant, was determined at the moderately high resolution of 2.0 A, while the tyrosine-to-tryptophan variant (Y98W) yielded very high resolution data (beyond 1.5 A) allowing a detailed look at the water structure, alternate side-chain conformations and the planarity of the FMN. Both structures were solved by molecular replacement beginning with the native (P2A) coordinates as a starting point. The Y98H variant of D. vulgaris flavodoxin crystallizes in space group P2(1)2(1)2(1), with unit-cell parameters a = 41.96, b = 61.45, c = 57.04 A, while the Y98W mutant adopts space group P2(1), with a = 41.29, b = 55.82, c = 32.52 A, beta = 100.68 degrees. Refinement for both mutants utilized PROLSQ followed by, for the high-resolution Y98W structure, anisotropic refinement as implemented in SHELXL. Final R factors of 17% for the Y98H mutant and 9.8% for the Y98W mutant were obtained. For the high-resolution (1.5 A) Y98W mutant, 31,010 unique reflections were collected from a single crystal. The final model includes 273 solvent molecules, with eight side chains assuming multiple conformations. At this resolution, the detailed conformation of the FMN can be observed, with both a bow and twist being noted. A comparison is made between the two mutants and the different oxidation states of the native flavodoxin. Although both mutants show similar E(2) (oxidized/semiquinone) one-electron redox potentials to the native, the E(1) (semiquinone/hydroquinone) redox potential for the Y98H mutant is significantly different from that of the Y98W variant and the native protein. The surprising similarity in the folding of the polypeptide chain 60--64 between the two mutants and the reduced states of the native is discussed. The interaction between O61 and N5 in the flavin is discussed because of the new conformation of this loop.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1F4P is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F4P OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Structures and comparison of the Y98H (2.0 A) and Y98W (1.5 A) mutants of flavodoxin (Desulfovibrio vulgaris)., Reynolds RA, Watt W, Watenpaugh KD, Acta Crystallogr D Biol Crystallogr. 2001 Apr;57(Pt 4):527-35. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11264581 11264581]
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| | [[Category: Desulfovibrio vulgaris]] | | [[Category: Desulfovibrio vulgaris]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Reynolds, R A.]] | + | [[Category: Reynolds RA]] |
| - | [[Category: Watenpaugh, K D.]] | + | [[Category: Watenpaugh KD]] |
| - | [[Category: Watt, W.]] | + | [[Category: Watt W]] |
| - | [[Category: 3d-strcture]]
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| - | [[Category: Anisotropic refinement]]
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| - | [[Category: Electron transport]]
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| - | [[Category: Flavoprotein]]
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| - | [[Category: Fmn]]
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| - | [[Category: Redox protein]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:53:50 2008''
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