1j9i

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{{Seed}}
 
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[[Image:1j9i.png|left|200px]]
 
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==STRUCTURE OF THE DNA BINDING DOMAIN OF THE GPNU1 SUBUNIT OF LAMBDA TERMINASE==
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The line below this paragraph, containing "STRUCTURE_1j9i", creates the "Structure Box" on the page.
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<StructureSection load='1j9i' size='340' side='right'caption='[[1j9i]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1j9i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J9I FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9i OCA], [https://pdbe.org/1j9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j9i RCSB], [https://www.ebi.ac.uk/pdbsum/1j9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j9i ProSAT]</span></td></tr>
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{{STRUCTURE_1j9i| PDB=1j9i | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TERS_LAMBD TERS_LAMBD] Component of the terminase that processes and encapsidates viral genomes during virion assembly. The terminase is composed of two small and one large subunits. To initiate packaging, it binds a specific sequence called cos, at the junction of adjacent viral genomes in the concatemeric DNA substrate. Next, in a reaction stimulated by the presence of proheads and ATP but not requiring ATP hydrolysis, the terminase creates two nicks 12bp appart at the cos site, one on each stand. Terminase then separates the cohesive ends in a reaction requiring ATP hydrolysis. The heterotrimer remains bound to the left end of the genome to be packaged, forming a stable DNA-protein complex known as complex I. In a reaction facilitated by a viral assembly catalyst, gpFI, complex I binds a prohead, a preformed head shell precursor, to form complex II. In another packaging reaction requiring ATP hydrolysis, the DNA is translocated into the prohead until the next cos site on the concatemer reaches the packaging complex. At this time the downstream cos site is cut and the heterotrimer undocks from the DNA-filled head to remain bound to the left end of concatemer's next genome. The new heterotrimer-DNA complex I binds another prohead to continue the processive, polarized packaging of viral genomes. The terminase is dependent upon host integration host factor (ihfA/ihfB) for these activities.<ref>PMID:2989542</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j9/1j9i_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1j9i ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Terminase enzymes mediate genome "packaging" during the reproduction of DNA viruses. In lambda, the gpNu1 subunit guides site-specific assembly of terminase onto DNA. The structure of the dimeric DNA binding domain of gpNu1 was solved using nuclear magnetic resonance spectroscopy. Its fold contains a unique winged helix-turn-helix (wHTH) motif within a novel scaffold. Surprisingly, a predicted P loop ATP binding motif is in fact the wing of the DNA binding motif. Structural and genetic analysis has identified determinants of DNA recognition specificity within the wHTH motif and the DNA recognition sequence. The structure reveals an unexpected DNA binding mode and provides a mechanistic basis for the concerted action of gpNu1 and Escherichia coli integration host factor during assembly of the packaging machinery.
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===STRUCTURE OF THE DNA BINDING DOMAIN OF THE GPNU1 SUBUNIT OF LAMBDA TERMINASE===
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Insights into specific DNA recognition during the assembly of a viral genome packaging machine.,de Beer T, Fang J, Ortega M, Yang Q, Maes L, Duffy C, Berton N, Sippy J, Overduin M, Feiss M, Catalano CE Mol Cell. 2002 May;9(5):981-91. PMID:12049735<ref>PMID:12049735</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1j9i" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_12049735}}, adds the Publication Abstract to the page
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*[[Terminase 3D Structures|Terminase 3D Structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 12049735 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12049735}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia virus Lambda]]
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1J9I is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J9I OCA].
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[[Category: Large Structures]]
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[[Category: Berton N]]
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==Reference==
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[[Category: Catalano C]]
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Insights into specific DNA recognition during the assembly of a viral genome packaging machine., de Beer T, Fang J, Ortega M, Yang Q, Maes L, Duffy C, Berton N, Sippy J, Overduin M, Feiss M, Catalano CE, Mol Cell. 2002 May;9(5):981-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12049735 12049735]
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[[Category: De Beer T]]
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[[Category: Enterobacteria phage lambda]]
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[[Category: Duffy C]]
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[[Category: Single protein]]
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[[Category: Feiss M]]
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[[Category: Beer, T De.]]
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[[Category: Maes L]]
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[[Category: Berton, N.]]
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[[Category: Meyer J]]
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[[Category: Catalano, C.]]
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[[Category: Ortega M]]
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[[Category: Duffy, C.]]
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[[Category: Overduin M]]
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[[Category: Feiss, M.]]
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[[Category: Sippy J]]
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[[Category: Maes, L.]]
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[[Category: Yang Q]]
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[[Category: Meyer, J.]]
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[[Category: Ortega, M.]]
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[[Category: Overduin, M.]]
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[[Category: Sippy, J.]]
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[[Category: Yang, Q.]]
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[[Category: Dna binding domain]]
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[[Category: Homodimer]]
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[[Category: Lambda]]
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[[Category: Terminase]]
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[[Category: Viral assembly]]
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[[Category: Winged helix-turn-helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 14:43:05 2008''
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Current revision

STRUCTURE OF THE DNA BINDING DOMAIN OF THE GPNU1 SUBUNIT OF LAMBDA TERMINASE

PDB ID 1j9i

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