2wc9: Difference between revisions
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< | ==Crystal structure of the g2p (large terminase) nuclease domain from the bacteriophage SPP1 with bound Mn== | ||
<StructureSection load='2wc9' size='340' side='right'caption='[[2wc9]], [[Resolution|resolution]] 2.50Å' scene=''> | |||
== Structural highlights == | |||
or the | <table><tr><td colspan='2'>[[2wc9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_phage_SPP1 Bacillus phage SPP1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WC9 FirstGlance]. <br> | ||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2wc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wc9 OCA], [https://pdbe.org/2wc9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wc9 RCSB], [https://www.ebi.ac.uk/pdbsum/2wc9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wc9 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/TERL_BPSPP TERL_BPSPP] 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). | |||
== 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/wc/2wc9_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2wc9 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The DNA-packaging motor in tailed bacteriophages requires nuclease activity to ensure that the genome is packaged correctly. This nuclease activity is tightly regulated as the enzyme is inactive for the duration of DNA translocation. Here, we report the X-ray structure of the large terminase nuclease domain from bacteriophage SPP1. Similarity with the RNase H family endonucleases allowed interactions with the DNA to be predicted. A structure-based alignment with the distantly related T4 gp17 terminase shows the conservation of an extended beta-sheet and an auxiliary beta-hairpin that are not found in other RNase H family proteins. The model with DNA suggests that the beta-hairpin partly blocks the active site, and in vivo activity assays show that the nuclease domain is not functional in the absence of the ATPase domain. Here, we propose that the nuclease activity is regulated by movement of the beta-hairpin, altering active site access and the orientation of catalytically essential residues. | |||
Structural basis for the nuclease activity of a bacteriophage large terminase.,Smits C, Chechik M, Kovalevskiy OV, Shevtsov MB, Foster AW, Alonso JC, Antson AA EMBO Rep. 2009 Jun;10(6):592-8. Epub 2009 May 15. PMID:19444313<ref>PMID:19444313</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2wc9" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Terminase 3D Structures|Terminase 3D Structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Bacillus phage SPP1]] | ||
[[ | [[Category: Large Structures]] | ||
[[Category: Alonso JC]] | |||
== | [[Category: Antson AA]] | ||
< | [[Category: Chechik M]] | ||
[[Category: Bacillus phage | [[Category: Foster AW]] | ||
[[Category: Alonso | [[Category: Kovalevskiy OV]] | ||
[[Category: Antson | [[Category: Shevtsov MB]] | ||
[[Category: Chechik | [[Category: Smits C]] | ||
[[Category: Foster | |||
[[Category: Kovalevskiy | |||
[[Category: Shevtsov | |||
[[Category: Smits | |||
Latest revision as of 12:34, 6 November 2024
Crystal structure of the g2p (large terminase) nuclease domain from the bacteriophage SPP1 with bound MnCrystal structure of the g2p (large terminase) nuclease domain from the bacteriophage SPP1 with bound Mn
Structural highlights
FunctionTERL_BPSPP 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). 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 PubMedThe DNA-packaging motor in tailed bacteriophages requires nuclease activity to ensure that the genome is packaged correctly. This nuclease activity is tightly regulated as the enzyme is inactive for the duration of DNA translocation. Here, we report the X-ray structure of the large terminase nuclease domain from bacteriophage SPP1. Similarity with the RNase H family endonucleases allowed interactions with the DNA to be predicted. A structure-based alignment with the distantly related T4 gp17 terminase shows the conservation of an extended beta-sheet and an auxiliary beta-hairpin that are not found in other RNase H family proteins. The model with DNA suggests that the beta-hairpin partly blocks the active site, and in vivo activity assays show that the nuclease domain is not functional in the absence of the ATPase domain. Here, we propose that the nuclease activity is regulated by movement of the beta-hairpin, altering active site access and the orientation of catalytically essential residues. Structural basis for the nuclease activity of a bacteriophage large terminase.,Smits C, Chechik M, Kovalevskiy OV, Shevtsov MB, Foster AW, Alonso JC, Antson AA EMBO Rep. 2009 Jun;10(6):592-8. Epub 2009 May 15. PMID:19444313[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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