4znl

From Proteopedia

(Difference between revisions)

Revision as of 07:34, 18 May 2023

Thermus Phage P74-26 Large Terminase ATPase domain bound to ADP Beryllium Fluoride

Structural highlights

4znl is a 3 chain structure with sequence from Thermus virus P74-26. 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

A7XXR1_BP742 The terminase large subunit acts as an ATP driven molecular motor necessary for viral DNA translocation into empty capsids and as an endonuclease that cuts the viral genome to initiate and to end a packaging reaction. The terminase lies at a unique vertex of the procapsid and is composed of two subunits, a small terminase subunit involved in viral DNA recognition (packaging sequence), and a large terminase subunit possessing endonucleolytic and ATPase activities. Both terminase subunits heterooligomerize and are docked on the portal protein to form the packaging machine. The terminase large subunit exhibits endonuclease activity and cleaves the viral genome concatemer. Once the capsid is packaged with the DNA, the terminase complex is substituted by the tail.[HAMAP-Rule:MF_04146]

Publication Abstract from PubMed

Many viruses package their genomes into procapsids using an ATPase machine that is among the most powerful known biological motors. However, how this motor couples ATP hydrolysis to DNA translocation is still unknown. Here, we introduce a model system with unique properties for studying motor structure and mechanism. We describe crystal structures of the packaging motor ATPase domain that exhibit nucleotide-dependent conformational changes involving a large rotation of an entire subdomain. We also identify the arginine finger residue that catalyzes ATP hydrolysis in a neighboring motor subunit, illustrating that previous models for motor structure need revision. Our findings allow us to derive a structural model for the motor ring, which we validate using small-angle X-ray scattering and comparisons with previously published data. We illustrate the model's predictive power by identifying the motor's DNA-binding and assembly motifs. Finally, we integrate our results to propose a mechanistic model for DNA translocation by this molecular machine.

Structure and mechanism of the ATPase that powers viral genome packaging.,Hilbert BJ, Hayes JA, Stone NP, Duffy CM, Sankaran B, Kelch BA Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):E3792-9. doi:, 10.1073/pnas.1506951112. Epub 2015 Jul 6. PMID:26150523^[1]

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

References

↑ Hilbert BJ, Hayes JA, Stone NP, Duffy CM, Sankaran B, Kelch BA. Structure and mechanism of the ATPase that powers viral genome packaging. Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):E3792-9. doi:, 10.1073/pnas.1506951112. Epub 2015 Jul 6. PMID:26150523 doi:http://dx.doi.org/10.1073/pnas.1506951112

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/4znl"

@@ Line 3: / Line 3: @@
 <StructureSection load='4znl' size='340' side='right'caption='[[4znl]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4znl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_phage_p74-26 Thermus phage p74-26]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZNL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZNL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4znl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_virus_P74-26 Thermus virus P74-26]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZNL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4zni|4zni]], [[4znj|4znj]], [[4znk|4znk]]</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=4znl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4znl OCA], [https://pdbe.org/4znl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4znl RCSB], [https://www.ebi.ac.uk/pdbsum/4znl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4znl ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">P74p84 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=466052 Thermus phage P74-26])</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=4znl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4znl OCA], [http://pdbe.org/4znl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4znl RCSB], [http://www.ebi.ac.uk/pdbsum/4znl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4znl ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A7XXR1_BP742 A7XXR1_BP742] The terminase large subunit acts as an ATP driven molecular motor necessary for viral DNA translocation into empty capsids and as an endonuclease that cuts the viral genome to initiate and to end a packaging reaction. The terminase lies at a unique vertex of the procapsid and is composed of two subunits, a small terminase subunit involved in viral DNA recognition (packaging sequence), and a large terminase subunit possessing endonucleolytic and ATPase activities. Both terminase subunits heterooligomerize and are docked on the portal protein to form the packaging machine. The terminase large subunit exhibits endonuclease activity and cleaves the viral genome concatemer. Once the capsid is packaged with the DNA, the terminase complex is substituted by the tail.[HAMAP-Rule:MF_04146]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 20: @@
 ==See Also==
-*[[Terminase|Terminase]]
+*[[Terminase 3D Structures|Terminase 3D Structures]]
 == References ==
 <references/>
@@ Line 26: / Line 26: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Thermus phage p74-26]]
+[[Category: Thermus virus P74-26]]
-[[Category: Duffy, C M]]
+[[Category: Duffy CM]]
-[[Category: Hayes, J A]]
+[[Category: Hayes JA]]
-[[Category: Hilbert, B J]]
+[[Category: Hilbert BJ]]
-[[Category: Kelch, B A]]
+[[Category: Kelch BA]]
-[[Category: Stone, N P]]
+[[Category: Stone NP]]
-[[Category: Dna translocation]]
-[[Category: Viral protein]]

4znl

From Proteopedia

Revision as of 07:34, 18 May 2023

Thermus Phage P74-26 Large Terminase ATPase domain bound to ADP Beryllium Fluoride

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