4dkw

From Proteopedia

(Difference between revisions)

Revision as of 08:23, 21 September 2022

Structure of P22 Large terminase nuclease domain

Structural highlights

4dkw is a 4 chain structure with sequence from Salmonella virus P22. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TERL_BPP22] Component of the molecular motor that translocates genomic DNA in empty capsid during DNA packaging. Heterodimerizes with small terminase protein to be docked on capsid portal protein. The latter forms a ring in which genomic DNA in translocated into the capsid. May have or induce an endonuclease activity to cleave the genome concatemer after encapsidation (By similarity).

Publication Abstract from PubMed

Packaging of viral genomes into preformed procapsids requires the controlled and synchronized activity of an ATPase and a genome-processing nuclease, both located in the large (L) terminase subunit. In this paper, we have characterized the structure and regulation of bacteriophage P22 L-terminase (gp2). Limited proteolysis reveals a bipartite organization, consisting of an N-terminal ATPase core flexibly connected to a C-terminal nuclease domain. The 2.02 A crystal structure of P22 headful nuclease obtained by in drop proteolysis of full length L-terminase (FL-L-terminase) reveals a central seven-stranded beta-sheet core that harbors two magnesium ions. Modeling studies with DNA suggest the two ions are poised for two-metal ion-dependent catalysis, but the nuclease DNA-binding surface is sterically hindered by a loop-helix (L1-alpha2) motif, which is incompatible with catalysis. Accordingly, the isolated nuclease is completely inactive in vitro, while it exhibits endonucleolytic activity in the context of FL-L-terminase. Deleting the auto-inhibitory L1-alpha2 motif (or just the loop L1) restores nuclease activity to a level comparable to FL-L-terminase. Together, these results suggest that the activity of P22 headful nuclease is regulated by an intramolecular cross-talk with the N-terminal ATPase domain. This cross-talk allows for precise and controlled cleavage of DNA that is essential for genome-packaging.

Structure of p22 headful packaging nuclease.,Roy A, Cingolani G J Biol Chem. 2012 Jun 19. PMID:22715098^[1]

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

References

↑ Roy A, Cingolani G. Structure of p22 headful packaging nuclease. J Biol Chem. 2012 Jun 19. PMID:22715098 doi:10.1074/jbc.M112.349894

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4dkw"

Categories: Large Structures | Salmonella virus P22 | Cingolani G | Roy A

@@ Line 1: / Line 1: @@
 ==Structure of P22 Large terminase nuclease domain==
-<StructureSection load='4dkw' size='340' side='right' caption='[[4dkw]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
+<StructureSection load='4dkw' size='340' side='right'caption='[[4dkw]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4dkw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpp22 Bpp22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DKW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4dkw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_virus_P22 Salmonella virus P22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DKW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">2, gene 2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10754 BPP22])</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=4dkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dkw OCA], [https://pdbe.org/4dkw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dkw RCSB], [https://www.ebi.ac.uk/pdbsum/4dkw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dkw ProSAT]</span></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=4dkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dkw OCA], [http://pdbe.org/4dkw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dkw RCSB], [http://www.ebi.ac.uk/pdbsum/4dkw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dkw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TERL_BPP22 TERL_BPP22]] Component of the molecular motor that translocates genomic DNA in empty capsid during DNA packaging. Heterodimerizes with small terminase protein to be docked on capsid portal protein. The latter forms a ring in which genomic DNA in translocated into the capsid. May have or induce an endonuclease activity to cleave the genome concatemer after encapsidation (By similarity).
+[[https://www.uniprot.org/uniprot/TERL_BPP22 TERL_BPP22]] Component of the molecular motor that translocates genomic DNA in empty capsid during DNA packaging. Heterodimerizes with small terminase protein to be docked on capsid portal protein. The latter forms a ring in which genomic DNA in translocated into the capsid. May have or induce an endonuclease activity to cleave the genome concatemer after encapsidation (By similarity).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 18: @@
 </div>
 <div class="pdbe-citations 4dkw" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Terminase 3D Structures|Terminase 3D Structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bpp22]]
+[[Category: Large Structures]]
-[[Category: Cingolani, G]]
+[[Category: Salmonella virus P22]]
-[[Category: Roy, A]]
+[[Category: Cingolani G]]
-[[Category: Dna]]
+[[Category: Roy A]]
-[[Category: Dna-packaging]]
-[[Category: Dna-packaging motor]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase]]
-[[Category: Large terminase]]
-[[Category: Nuclease fold]]
-[[Category: Small terminase]]

4dkw

From Proteopedia

Revision as of 08:23, 21 September 2022

Structure of P22 Large terminase nuclease domain

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox