1gpc: Difference between revisions

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 ==CORE GP32, DNA-BINDING PROTEIN==
-<StructureSection load='1gpc' size='340' side='right' caption='[[1gpc]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='1gpc' size='340' side='right'caption='[[1gpc]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1gpc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GPC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1gpc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GPC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 2.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GENE 32 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1gpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gpc RCSB], [http://www.ebi.ac.uk/pdbsum/1gpc PDBsum]</span></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=1gpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gpc OCA], [https://pdbe.org/1gpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gpc RCSB], [https://www.ebi.ac.uk/pdbsum/1gpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gpc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VHED_BPT4 VHED_BPT4]] Binds preferentially to single-stranded DNA and therefore, destabilizes double-stranded DNA. It is involved in DNA replication, repair and recombination. Binds ss-DNA as the replication fork advances and stimulates the replisome processivity and accuracy.
+[https://www.uniprot.org/uniprot/SSB_BPT4 SSB_BPT4] Single-stranded DNA-binding protein that participates in viral DNA replication, recombination, and repair (Probable). Coats the lagging-strand ssDNA as the replication fork advances (PubMed:9079662). Stimulates the activities of viral DNA polymerase and DnaB-like SF4 replicative helicase, probably via its interaction with the helicase assembly factor (PubMed:14871889). Together with DnaB-like SF4 replicative helicase and the helicase assembly factor, promotes pairing of two homologous DNA molecules containing complementary single-stranded regions and mediates homologous DNA strand exchange (PubMed:11459967). Promotes also the formation of joint molecules (PubMed:9079662). mRNA specific autogenous translational repressor (PubMed:15507125).[HAMAP-Rule:MF_04152]<ref>PMID:11459967</ref> <ref>PMID:14871889</ref> <ref>PMID:15507125</ref> <ref>PMID:9079662</ref> <ref>PMID:9079662</ref>
 == 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/gp/1gpc_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gp/1gpc_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/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=1gpc ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The single-stranded DNA (ssDNA) binding protein gp32 from bacteriophage T4 is essential for T4 DNA replication, recombination and repair. In vivo gp32 binds ssDNA as the replication fork advances and stimulates replisome processivity and accuracy by a factor of several hundred. Gp32 binding affects nearly every major aspect of DNA metabolism. Among its important functions are: (1) configuring ssDNA templates for efficient use by the replisome including DNA polymerase; (2) melting out adventitious secondary structures; (3) protecting exposed ssDNA from nucleases; and (4) facilitating homologous recombination by binding ssDNA during strand displacement. We have determined the crystal structure of the gp32 DNA binding domain complexed to ssDNA at 2.2 A resolution. The ssDNA binding cleft comprises regions from three structural subdomains and includes a positively charged surface that runs parallel to a series of hydrophobic pockets formed by clusters of aromatic side chains. Although only weak electron density is seen for the ssDNA, it indicates that the phosphate backbone contacts an electropositive cleft of the protein, placing the bases in contact with the hydrophobic pockets. The DNA mobility implied by the weak electron density may reflect the role of gp32 as a sequence-independent ssDNA chaperone allowing the largely unstructured ssDNA to slide freely through the cleft.
-Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA.,Shamoo Y, Friedman AM, Parsons MR, Konigsberg WH, Steitz TA Nature. 1995 Jul 27;376(6538):362-6. PMID:7630406<ref>PMID:7630406</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==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__
 </StructureSection>
-[[Category: Enterobacteria phage t4]]
+[[Category: Escherichia virus T4]]
-[[Category: Friedman, A M]]
+[[Category: Large Structures]]
-[[Category: Konigsberg, W H]]
+[[Category: Friedman AM]]
-[[Category: Parsons, M R]]
+[[Category: Konigsberg WH]]
-[[Category: Shamoo, Y]]
+[[Category: Parsons MR]]
-[[Category: Steitz, T A]]
+[[Category: Shamoo Y]]
-[[Category: Dna binding protein-dna complex]]
+[[Category: Steitz TA]]
-[[Category: Single-stranded dna-binding]]
-[[Category: Ssb]]
-[[Category: Zinc binding domain]]