1f4p: Difference between revisions

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New page: left|200px<br /><applet load="1f4p" size="450" color="white" frame="true" align="right" spinBox="true" caption="1f4p, resolution 1.3Å" /> '''Y98W FLAVODOXIN MUTAN...
 
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[[Image:1f4p.gif|left|200px]]<br /><applet load="1f4p" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1f4p, resolution 1.3&Aring;" />
'''Y98W FLAVODOXIN MUTANT 1.5A (D. VULGARIS)'''<br />


==Overview==
==Y98W FLAVODOXIN MUTANT 1.5A (D. VULGARIS)==
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.
<StructureSection load='1f4p' size='340' side='right'caption='[[1f4p]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
<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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</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>
<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>


==About this Structure==
==See Also==
1F4P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with FMN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1F4P OCA].
*[[Flavodoxin 3D structures|Flavodoxin 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=11264581 11264581]
[[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: FMN]]
[[Category: 3d-strcture]]
[[Category: anisotropic refinement]]
[[Category: electron transport]]
[[Category: flavoprotein]]
[[Category: fmn]]
[[Category: redox protein]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:36:55 2007''

Latest revision as of 10:10, 7 February 2024

Y98W FLAVODOXIN MUTANT 1.5A (D. VULGARIS)Y98W FLAVODOXIN MUTANT 1.5A (D. VULGARIS)

Structural highlights

1f4p is a 1 chain structure with sequence from Desulfovibrio vulgaris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.3Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FLAV_DESVH Low-potential electron donor to a number of redox enzymes.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1f4p, resolution 1.30Å

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