2gva: Difference between revisions
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< | ==REFINED SOLUTION STRUCTURE OF THE TYR 41--> HIS MUTANT OF THE M13 GENE V PROTEIN. A COMPARISON WITH THE CRYSTAL STRUCTURE== | ||
<StructureSection load='2gva' size='340' side='right'caption='[[2gva]]' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2gva]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_M13 Escherichia virus M13]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1gva 1gva]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GVA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GVA FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2gva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gva OCA], [https://pdbe.org/2gva PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gva RCSB], [https://www.ebi.ac.uk/pdbsum/2gva PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gva ProSAT]</span></td></tr> | ||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/G5P_BPM13 G5P_BPM13] 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. | |||
== 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/gv/2gva_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=2gva ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The three-dimensional solution structure of mutant Tyr41-->His of the single-stranded DNA binding protein encoded by gene V of the filamentous bacteriophage M13 has been refined in two stages. The first stage involved the collection of additional NOE-based distance constraints, which were then used in eight cycles of back-calculations and structure calculations. The structures of the gene V protein dimers were calculated using simulated annealing, employing restrained molecular dynamics with a geometric force field. In the second stage of the refinement procedure, solvent was explicitly included during the dynamic calculations. A total of 30 structures was calculated for the protein, representing its solution structure in water. The first calculation step significantly improved the convergence of the structures, whereas the subsequent simulations in water made the structures physically more realistic. This is, for instance, illustrated by the number of hydrogen bonds formed in the molecule, which increased considerably upon going to aqueous solution. It is shown that the solution structure of the mutant gene V protein is nearly identical to the crystal structure of the wild-type molecule, except for the DNA-binding loop (residues 16-28). This antiparallel beta-hairpin is twisted and partially folded back towards the core of the protein in the NMR structure, whereas it is more extended and points away from the rest of the molecule in the X-ray structure. Unrestrained molecular dynamics calculations suggest that this latter conformation is energetically unstable in solution. | |||
Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure.,Prompers JJ, Folmer RH, Nilges M, Folkers PJ, Konings RN, Hilbers CW Eur J Biochem. 1995 Sep 1;232(2):506-14. PMID:7556200<ref>PMID:7556200</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2gva" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Single-stranded DNA-binding protein 3D structures|Single-stranded DNA-binding protein 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Escherichia virus M13]] | ||
[[Category: Large Structures]] | |||
[[Category: Folkers PJM]] | |||
== | [[Category: Folmer RHA]] | ||
< | [[Category: Hilbers CW]] | ||
[[Category: | [[Category: Konings RNH]] | ||
[[Category: Folkers | [[Category: Nilges M]] | ||
[[Category: Folmer | [[Category: Prompers JJ]] | ||
[[Category: Hilbers | |||
[[Category: Konings | |||
[[Category: Nilges | |||
[[Category: Prompers | |||
Latest revision as of 22:00, 29 May 2024
REFINED SOLUTION STRUCTURE OF THE TYR 41--> HIS MUTANT OF THE M13 GENE V PROTEIN. A COMPARISON WITH THE CRYSTAL STRUCTUREREFINED SOLUTION STRUCTURE OF THE TYR 41--> HIS MUTANT OF THE M13 GENE V PROTEIN. A COMPARISON WITH THE CRYSTAL STRUCTURE
Structural highlights
FunctionG5P_BPM13 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. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe three-dimensional solution structure of mutant Tyr41-->His of the single-stranded DNA binding protein encoded by gene V of the filamentous bacteriophage M13 has been refined in two stages. The first stage involved the collection of additional NOE-based distance constraints, which were then used in eight cycles of back-calculations and structure calculations. The structures of the gene V protein dimers were calculated using simulated annealing, employing restrained molecular dynamics with a geometric force field. In the second stage of the refinement procedure, solvent was explicitly included during the dynamic calculations. A total of 30 structures was calculated for the protein, representing its solution structure in water. The first calculation step significantly improved the convergence of the structures, whereas the subsequent simulations in water made the structures physically more realistic. This is, for instance, illustrated by the number of hydrogen bonds formed in the molecule, which increased considerably upon going to aqueous solution. It is shown that the solution structure of the mutant gene V protein is nearly identical to the crystal structure of the wild-type molecule, except for the DNA-binding loop (residues 16-28). This antiparallel beta-hairpin is twisted and partially folded back towards the core of the protein in the NMR structure, whereas it is more extended and points away from the rest of the molecule in the X-ray structure. Unrestrained molecular dynamics calculations suggest that this latter conformation is energetically unstable in solution. Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure.,Prompers JJ, Folmer RH, Nilges M, Folkers PJ, Konings RN, Hilbers CW Eur J Biochem. 1995 Sep 1;232(2):506-14. PMID:7556200[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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