5m1q - Revision history

OCA at 07:25, 1 May 2024

2024-05-01T07:25:56Z

←Older revision		Revision as of 07:25, 1 May 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/TERL_BPG20 TERL_BPG20]		[https://www.uniprot.org/uniprot/TERL_BPG20 TERL_BPG20]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Bacteriophages and large dsDNA viruses encode sophisticated machinery to translocate their DNA into a preformed empty capsid. An essential part of this machine, the large terminase protein, processes viral DNA into constituent units utilizing its nuclease activity. Crystal structures of the large terminase nuclease from the thermophilic bacteriophage G20c show that it is most similar to the RuvC family of the RNase H-like endonucleases. Like RuvC proteins, the nuclease requires either Mn2+, Mg2+ or Co2+ ions for activity, but is inactive with Zn2+ and Ca2+ High resolution crystal structures of complexes with different metals reveal that in the absence of DNA, only one catalytic metal ion is accommodated in the active site. Binding of the second metal ion may be facilitated by conformational variability, which enables the two catalytic aspartic acids to be brought closer to each other. Structural comparison indicates that in common with the RuvC family, the location of the two catalytic metals differs from other members of the RNase H family. In contrast to a recently proposed mechanism, the available data do not support binding of the two metals at an ultra-short interatomic distance. Thus we postulate that viral terminases cleave DNA by the canonical RuvC-like mechanism.
-
-	Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism.,Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive SJ, Antson AA Nucleic Acids Res. 2017 Jan 18. pii: gkw1354. doi: 10.1093/nar/gkw1354. PMID:28100693<ref>PMID:28100693</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5m1q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Terminase 3D Structures\|Terminase 3D Structures]]		*[[Terminase 3D Structures\|Terminase 3D Structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:20, 1 November 2023

2023-11-01T18:20:11Z

←Older revision		Revision as of 18:20, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='5m1q' size='340' side='right'caption='[[5m1q]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='5m1q' size='340' side='right'caption='[[5m1q]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m1q]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpg20 Bpg20~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M1Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5M1Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m1q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_phage_G20c Thermus phage G20c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M1Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.45Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5m1p\|5m1p]], [[5m1o\|5m1o]], [[5m1n\|5m1n]], [[5m1k\|5m1k]], [[5m1f\|5m1f]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5m1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1q OCA], [~~http~~://pdbe.org/5m1q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5m1q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5m1q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1q ProSAT]</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=5m1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1q OCA], [https://pdbe.org/5m1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m1q RCSB], [https://www.ebi.ac.uk/pdbsum/5m1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TERL_BPG20 TERL_BPG20]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:

	==See Also==		==See Also==
-	*[[Terminase\|Terminase]]	+	*[[Terminase 3D Structures\|Terminase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bpg20]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Antson~~, A A~~]]	+	[[Category: Thermus phage G20c]]
-	[[Category: Blagova~~, E V~~]]	+	[[Category: Antson AA]]
-	[[Category: Chechik, M]]	+	[[Category: Blagova EV]]
-	[[Category: Greive~~, S J~~]]	+	[[Category: Chechik M]]
-	[[Category: Jenkins~~, H T~~]]	+	[[Category: Greive SJ]]
-	[[Category: Xu~~, R G]]~~	+	[[Category: Jenkins HT]]
-	~~[[Category: Large terminase]]~~	+	[[Category: Xu RG]]
-	~~[[Category: Nuclease domain]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 10:58, 12 August 2020

2020-08-12T10:58:49Z

←Older revision		Revision as of 10:58, 12 August 2020
Line 1:		Line 1:

	==Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound Zinc==		==Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound Zinc==
-	<StructureSection load='5m1q' size='340' side='right' caption='[[5m1q]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='5m1q' size='340' side='right'caption='[[5m1q]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5m1q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M1Q OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5M1Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5m1q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpg20 Bpg20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M1Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5M1Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5m1p\|5m1p]], [[5m1o\|5m1o]], [[5m1n\|5m1n]], [[5m1k\|5m1k]], [[5m1f\|5m1f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5m1p\|5m1p]], [[5m1o\|5m1o]], [[5m1n\|5m1n]], [[5m1k\|5m1k]], [[5m1f\|5m1f]]</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=5m1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1q OCA], [http://pdbe.org/5m1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m1q RCSB], [http://www.ebi.ac.uk/pdbsum/5m1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1q ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5m1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1q OCA], [http://pdbe.org/5m1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m1q RCSB], [http://www.ebi.ac.uk/pdbsum/5m1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1q ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5m1q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5m1q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Terminase\|Terminase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpg20]]
		+	[[Category: Large Structures]]
	[[Category: Antson, A A]]		[[Category: Antson, A A]]
	[[Category: Blagova, E V]]		[[Category: Blagova, E V]]

OCA at 10:59, 1 February 2017

2017-02-01T10:59:12Z

←Older revision		Revision as of 10:59, 1 February 2017
Line 8:		Line 8:
	<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=5m1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1q OCA], [http://pdbe.org/5m1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m1q RCSB], [http://www.ebi.ac.uk/pdbsum/5m1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1q 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=5m1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1q OCA], [http://pdbe.org/5m1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m1q RCSB], [http://www.ebi.ac.uk/pdbsum/5m1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1q ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteriophages and large dsDNA viruses encode sophisticated machinery to translocate their DNA into a preformed empty capsid. An essential part of this machine, the large terminase protein, processes viral DNA into constituent units utilizing its nuclease activity. Crystal structures of the large terminase nuclease from the thermophilic bacteriophage G20c show that it is most similar to the RuvC family of the RNase H-like endonucleases. Like RuvC proteins, the nuclease requires either Mn2+, Mg2+ or Co2+ ions for activity, but is inactive with Zn2+ and Ca2+ High resolution crystal structures of complexes with different metals reveal that in the absence of DNA, only one catalytic metal ion is accommodated in the active site. Binding of the second metal ion may be facilitated by conformational variability, which enables the two catalytic aspartic acids to be brought closer to each other. Structural comparison indicates that in common with the RuvC family, the location of the two catalytic metals differs from other members of the RNase H family. In contrast to a recently proposed mechanism, the available data do not support binding of the two metals at an ultra-short interatomic distance. Thus we postulate that viral terminases cleave DNA by the canonical RuvC-like mechanism.
		+
		+	Viral genome packaging terminase cleaves DNA using the canonical RuvC-like two-metal catalysis mechanism.,Xu RG, Jenkins HT, Chechik M, Blagova EV, Lopatina A, Klimuk E, Minakhin L, Severinov K, Greive SJ, Antson AA Nucleic Acids Res. 2017 Jan 18. pii: gkw1354. doi: 10.1093/nar/gkw1354. PMID:28100693<ref>PMID:28100693</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5m1q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:49, 26 October 2016

2016-10-26T18:49:48Z

←Older revision		Revision as of 18:49, 26 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5m1q is ON HOLD~~	+	==Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound Zinc==
-		+	<StructureSection load='5m1q' size='340' side='right' caption='[[5m1q]], [[Resolution\|resolution]] 1.45Å' scene=''>
-	~~Authors: Xu, R.G., Jenkins, H.T., Chechik, M., Blagova, E.V., Greive, S.J., Antson, A.A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5m1q]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5M1Q FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound Zinc	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5m1p\|5m1p]], [[5m1o\|5m1o]], [[5m1n\|5m1n]], [[5m1k\|5m1k]], [[5m1f\|5m1f]]</td></tr>
-	[[~~Category~~: ~~Greive~~, ~~S.J~~]]	+	<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=5m1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m1q OCA], [http://pdbe.org/5m1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5m1q RCSB], [http://www.ebi.ac.uk/pdbsum/5m1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5m1q ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Blagova~~, E.V]]	+	</table>
-	[[Category: Antson, A.A]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Antson, A A]]
		+	[[Category: Blagova, E V]]
	[[Category: Chechik, M]]		[[Category: Chechik, M]]
-	[[Category: Xu, ~~R.G~~]]	+	[[Category: Greive, S J]]
-	[[Category: Jenkins, H.T]]	+	[[Category: Jenkins, H T]]
		+	[[Category: Xu, R G]]
		+	[[Category: Large terminase]]
		+	[[Category: Nuclease domain]]
		+	[[Category: Viral protein]]

OCA: Protected "5m1q" [edit=sysop:move=sysop]

2016-10-19T15:04:04Z

Protected "5m1q" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:04, 19 October 2016

OCA: New page: '''Unreleased structure''' The entry 5m1q is ON HOLD Authors: Xu, R.G., Jenkins, H.T., Chechik, M., Blagova, E.V., Greive, S.J., Antson, A.A. Description: Crystal structure of the larg...

2016-10-19T15:04:02Z

New page: '''Unreleased structure''' The entry 5m1q is ON HOLD Authors: Xu, R.G., Jenkins, H.T., Chechik, M., Blagova, E.V., Greive, S.J., Antson, A.A. Description: Crystal structure of the larg...

New page

'''Unreleased structure'''

The entry 5m1q is ON HOLD

Authors: Xu, R.G., Jenkins, H.T., Chechik, M., Blagova, E.V., Greive, S.J., Antson, A.A.

Description: Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound Zinc
[[Category: Unreleased Structures]]
[[Category: Greive, S.J]]
[[Category: Blagova, E.V]]
[[Category: Antson, A.A]]
[[Category: Chechik, M]]
[[Category: Xu, R.G]]
[[Category: Jenkins, H.T]]