1vqf: Difference between revisions

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New page: left|200px<br /><applet load="1vqf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vqf, resolution 1.8Å" /> '''GENE V PROTEIN MUTANT...
 
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[[Image:1vqf.jpg|left|200px]]<br /><applet load="1vqf" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1vqf, resolution 1.8&Aring;" />
'''GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 AND ILE 47 REPLACED BY VAL 47 (V35I, I47V)'''<br />


==Overview==
==GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 AND ILE 47 REPLACED BY VAL 47 (V35I, I47V)==
The basis for the context dependence of the effects of core mutations on, protein stability was investigated by comparing the structures of three, gene V protein mutants with that of the wild-type protein. We previously, examined a "swapped" mutant in which core residues Val35 and Ile47 were, simply reversed so that the mutant had no hydrophobicity change from the, native protein. The swapped mutant was destabilized by 3 kcal/mol per gene, V protein dimer relative to the wild-type protein, demonstrating that, factors other than hydrophobicity must make substantial contributions to, the effects of mutations on the stability of the protein. Here we have, determined the structure of this swapped mutant (V35I/I47V) as well as, those of the two constituent mutants (V35I and I47V). We find that the, structures of the mutant proteins are very similar to that of the, wild-type protein except for the necessary addition or deletion of, methylene groups and for slight positional shifts of atoms around each, mutated residue. The structure of the double mutant is a composite of the, structures of the two single mutants. In the mutant structures, the V35I, mutation fills a cavity that exists in the wild-type protein and the I47V, mutation creates a new cavity. The structures of the mutants indicate, further that the reason the V35I and I47V mutations do not have opposite, effects on stability is that the cavity in the wild-type protein filled by, the V35I mutation is not optimally shaped for accommodating the additional, methylene group of the isoleucine. These results support the concepts that, the details of core packing have substantial influence on the effects of, core mutations on protein stability and that these packing effects are, major determinants of the context dependence of core mutation effects on, stability.
<StructureSection load='1vqf' size='340' side='right'caption='[[1vqf]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1vqf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_f1 Enterobacteria phage f1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VQF 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]] 1.8&#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=1vqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vqf OCA], [https://pdbe.org/1vqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vqf RCSB], [https://www.ebi.ac.uk/pdbsum/1vqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vqf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/G5P_BPF1 G5P_BPF1] Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity).
== 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/vq/1vqf_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=1vqf ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1VQF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_f1 Bacteriophage f1]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VQF OCA].
*[[Single-stranded DNA-binding protein 3D structures|Single-stranded DNA-binding protein 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Context dependence of mutational effects in a protein: the crystal structures of the V35I, I47V and V35I/I47V gene V protein core mutants., Zhang H, Skinner MM, Sandberg WS, Wang AH, Terwilliger TC, J Mol Biol. 1996 May 31;259(1):148-59. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8648642 8648642]
[[Category: Enterobacteria phage f1]]
[[Category: Bacteriophage f1]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Sandberg WS]]
[[Category: Sandberg, W.S.]]
[[Category: Skinner MM]]
[[Category: Skinner, M.M.]]
[[Category: Terwilliger TC]]
[[Category: Terwilliger, T.C.]]
[[Category: Wang AH-J]]
[[Category: Wang, A.H.J.]]
[[Category: Zhang H]]
[[Category: Zhang, H.]]
[[Category: dna-binding protein]]
[[Category: gene v]]
[[Category: mutant]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:02:34 2007''

Latest revision as of 11:46, 14 February 2024

GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 AND ILE 47 REPLACED BY VAL 47 (V35I, I47V)GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 AND ILE 47 REPLACED BY VAL 47 (V35I, I47V)

Structural highlights

1vqf is a 1 chain structure with sequence from Enterobacteria phage f1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G5P_BPF1 Binds to DNA in a highly cooperative manner without pronounced sequence specificity. During synthesis of the single-stranded (progeny) viral DNA, prevents the conversion into the double-stranded replicative form. G5P is displaced by the capsid protein G8P during phage assembly on the inner bacterial membrane (By similarity).

Evolutionary Conservation

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

See Also

1vqf, resolution 1.80Å

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