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==REFINED STRUCTURE OF THE GENE 5 DNA BINDING PROTEIN FROM BACTERIOPHAGE FD==
==REFINED STRUCTURE OF THE GENE 5 DNA BINDING PROTEIN FROM BACTERIOPHAGE FD==
<StructureSection load='2gn5' size='340' side='right' caption='[[2gn5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='2gn5' size='340' side='right'caption='[[2gn5]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2gn5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpm13 Bpm13]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1gn5 1gn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GN5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GN5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2gn5]] is a 1 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=1gn5 1gn5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GN5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GN5 FirstGlance]. <br>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gn5 OCA], [http://pdbe.org/2gn5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gn5 RCSB], [http://www.ebi.ac.uk/pdbsum/2gn5 PDBsum]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#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=2gn5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gn5 OCA], [https://pdbe.org/2gn5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gn5 RCSB], [https://www.ebi.ac.uk/pdbsum/2gn5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gn5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/G5P_BPFD G5P_BPFD]] 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).  
[https://www.uniprot.org/uniprot/G5P_BPFD G5P_BPFD] 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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gn/2gn5_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gn/2gn5_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=2gn5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional structure of the gene 5 DNA binding protein (G5BP) from bacteriophage fd has been determined from a combination of multiple isomorphous replacement techniques, partial refinements and deleted fragment difference Fourier syntheses. The structure was refined using restrained parameter least-squares and difference Fourier methods to a final residual of R = 0.217 for the 3528 statistically significant reflections present to 2.3 A resolution. In addition to the 682 atoms of the protein, 12 solvent molecules were included. We describe here the dispositions and orientations of the amino acid side-chains and their interactions as visualized in the G5BP structure. The G5BP monomer of 87 peptide units is almost entirely in the beta-conformation, organized as a three-stranded sheet, a two-stranded beta-ribbon and a broad connecting loop. There is no alpha-helix present in the molecule. Two G5BP monomers are tightly interlocked about an intermolecular dyad axis to form a compact dimer unit of about 55 A X 45 A X 36 A. The dimer is characterized by two symmetry-related antiparallel clefts that traverse the monomer surfaces essentially perpendicular to the dyad axis. From the three-stranded antiparallel beta-sheet, formed from the first two-thirds of the sequence, extend three tyrosine residues (26, 34, 41), a lysine (46) and two arginine residues (16, 21) that, as indicated by other physical and chemical experiments, are directly involved in DNA binding. Other residues likely to share binding responsibility are arginine 80 extending from the beta-ribbon and phenylalanine 73 from the tip of this loop, but as provided, however, by the opposite monomer within each G5BP dimer pair. Thus, both symmetry-related DNA binding sites have a composite nature and include contributions from both elements of the dimer. The gene 5 dimer is clearly the active binding species, and the two monomers within the dyad-related pair are so structurally contiguous that one cannot be certain whether the isolated monomer would maintain its observed crystal structure. This linkage is manifested primarily as a skeletal core of hydrophobic residues that extends from the center of each monomer continuously through an intermolecular beta-barrel that joins the pair. Protruding from the major area of density of each monomer is an elongated wing of tenuous structure comprising residues 15 through 32, which is, we believe, intimately involved in DNA binding. This wing appears to be dynamic and mobile, even in the crystal and, therefore, is likely to undergo conformational change in the presence of the ligand.
Refined structure of the gene 5 DNA binding protein from bacteriophage fd.,Brayer GD, McPherson A J Mol Biol. 1983 Sep 15;169(2):565-96. PMID:6684697<ref>PMID:6684697</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2gn5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Single-stranded DNA-binding protein|Single-stranded DNA-binding protein]]
*[[Single-stranded DNA-binding protein 3D structures|Single-stranded DNA-binding protein 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bpm13]]
[[Category: Escherichia virus M13]]
[[Category: Brayer, G D]]
[[Category: Large Structures]]
[[Category: McPherson, A]]
[[Category: Brayer GD]]
[[Category: McPherson A]]

Latest revision as of 12:28, 14 February 2024

REFINED STRUCTURE OF THE GENE 5 DNA BINDING PROTEIN FROM BACTERIOPHAGE FDREFINED STRUCTURE OF THE GENE 5 DNA BINDING PROTEIN FROM BACTERIOPHAGE FD

Structural highlights

2gn5 is a 1 chain structure with sequence from Escherichia virus M13. This structure supersedes the now removed PDB entry 1gn5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G5P_BPFD 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

2gn5, resolution 2.30Å

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