1j9i

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

1j9i is a 2 chain structure with sequence from Escherichia virus Lambda. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1]

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 PubMed

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.

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Frackman S, Siegele DA, Feiss M. The terminase of bacteriophage lambda. Functional domains for cosB binding and multimer assembly. J Mol Biol. 1985 May 25;183(2):225-38. PMID:2989542 doi:http://dx.doi.org/10.1016/0022-2836(85)90215-3
↑ de Beer T, Fang J, Ortega M, Yang Q, Maes L, Duffy C, Berton N, Sippy J, Overduin M, Feiss M, Catalano CE. Insights into specific DNA recognition during the assembly of a viral genome packaging machine. Mol Cell. 2002 May;9(5):981-91. PMID:12049735

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1j9i"

@@ Line 1: / Line 1: @@
 ==STRUCTURE OF THE DNA BINDING DOMAIN OF THE GPNU1 SUBUNIT OF LAMBDA TERMINASE==
-<StructureSection load='1j9i' size='340' side='right' caption='[[1j9i]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1j9i' size='340' side='right'caption='[[1j9i]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1j9i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J9I FirstGlance]. <br>
+<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>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</td></tr>
+</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j9i OCA], [http://pdbe.org/1j9i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j9i RCSB], [http://www.ebi.ac.uk/pdbsum/1j9i 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=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>
 </table>
 == Function ==
-[[http://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>
+[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>
 == 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/j9/1j9i_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j9/1j9i_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=1j9i ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 </div>
 <div class="pdbe-citations 1j9i" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Terminase 3D Structures|Terminase 3D Structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteriophage lambda]]
+[[Category: Escherichia virus Lambda]]
-[[Category: Beer, T De]]
+[[Category: Large Structures]]
-[[Category: Berton, N]]
+[[Category: Berton N]]
-[[Category: Catalano, C]]
+[[Category: Catalano C]]
-[[Category: Duffy, C]]
+[[Category: De Beer T]]
-[[Category: Feiss, M]]
+[[Category: Duffy C]]
-[[Category: Maes, L]]
+[[Category: Feiss M]]
-[[Category: Meyer, J]]
+[[Category: Maes L]]
-[[Category: Ortega, M]]
+[[Category: Meyer J]]
-[[Category: Overduin, M]]
+[[Category: Ortega M]]
-[[Category: Sippy, J]]
+[[Category: Overduin M]]
-[[Category: Yang, Q]]
+[[Category: Sippy J]]
-[[Category: Dna binding domain]]
+[[Category: Yang Q]]
-[[Category: Homodimer]]
-[[Category: Lambda]]
-[[Category: Terminase]]
-[[Category: Viral assembly]]
-[[Category: Viral protein]]
-[[Category: Winged helix-turn-helix]]

1j9i

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox