6uke - Revision history

OCA at 14:57, 13 March 2024

2024-03-13T14:57:31Z

← Older revision		Revision as of 14:57, 13 March 2024
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	<StructureSection load='6uke' size='340' side='right'caption='[[6uke]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='6uke' size='340' side='right'caption='[[6uke]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6uke]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_10014 Atcc 10014~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UKE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6UKE FirstGlance]. <br>		<table><tr><td colspan='2'>[[6uke]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_parahaemolyticus Haemophilus parahaemolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UKE FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'>ACT</scene~~>, ~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.62Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene><~~/td~~></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"~~>~~HMPREF1050_0931 ([http:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=735 ATCC 10014])~~</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=6uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uke OCA], [https://pdbe.org/6uke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uke RCSB], [https://www.ebi.ac.uk/pdbsum/6uke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uke 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=6uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uke OCA], [~~http~~://pdbe.org/6uke PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6uke RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6uke PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6uke ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style~~=~~"background-color:#fffaf0;">~~		== Function ==
	=~~= Publication Abstract from PubMed~~ ==		[https://www.uniprot.org/uniprot/I3DBY6_HAEPH I3DBY6_HAEPH]
	~~HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG downward arrowC-3' in duplex DNA and cleaves (' downward arrow') to produce fragments with 2-base, 3'-overhangs~~. ~~We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1~~.0 A. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded beta sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the 'PD-D/EXK' superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G downward arrowCGC) and MspI (C downward arrowCGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.

	Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 A.,Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X Nucleic Acids Res. 2019 Dec 27. pii: 5687824. doi: 10.1093/nar/gkz1195. PMID:31879785<ref>PMID:31879785</ref>		==See Also==
			*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6uke" style="background-color:#fffaf0;"></div>~~
	== ~~References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Atcc 10014~~]]		[[Category: Haemophilus parahaemolyticus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Cheng, X]]		[[Category: Cheng X]]
	[[Category: Horton~~, J R]]~~		[[Category: Horton JR]]
	~~[[Category: Hydrolase-dna complex]]~~
	~~[[Category: Iodine phasing]]~~
	~~[[Category: Modification]]~~
	~~[[Category: Protein-dna complex]]~~
	~~[[Category: Restriction~~]]

OCA at 09:49, 8 January 2020

2020-01-08T09:49:45Z

← Older revision		Revision as of 09:49, 8 January 2020
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	<StructureSection load='6uke' size='340' side='right'caption='[[6uke]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='6uke' size='340' side='right'caption='[[6uke]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6uke]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UKE FirstGlance]. <br>		<table><tr><td colspan='2'>[[6uke]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_10014 Atcc 10014]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UKE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HMPREF1050_0931 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=735 ATCC 10014])</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=6uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uke OCA], [http://pdbe.org/6uke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uke RCSB], [http://www.ebi.ac.uk/pdbsum/6uke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uke 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=6uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uke OCA], [http://pdbe.org/6uke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uke RCSB], [http://www.ebi.ac.uk/pdbsum/6uke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uke ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG downward arrowC-3' in duplex DNA and cleaves (' downward arrow') to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 A. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded beta sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the 'PD-D/EXK' superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G downward arrowCGC) and MspI (C downward arrowCGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.

			Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 A.,Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X Nucleic Acids Res. 2019 Dec 27. pii: 5687824. doi: 10.1093/nar/gkz1195. PMID:31879785<ref>PMID:31879785</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6uke" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Atcc 10014]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Cheng, X]]		[[Category: Cheng, X]]

OCA at 08:00, 18 December 2019

2019-12-18T08:00:57Z

← Older revision		Revision as of 08:00, 18 December 2019
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6uke is ~~ON HOLD until Paper Publication~~		==HhaI endonuclease in Complex with Iodine-Labelled DNA==
			<StructureSection load='6uke' size='340' side='right'caption='[[6uke]], [[Resolution\|resolution]] 1.62Å' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>[[6uke]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UKE FirstGlance]. <br>
	~~Description~~:		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></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=6uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uke OCA], [http://pdbe.org/6uke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uke RCSB], [http://www.ebi.ac.uk/pdbsum/6uke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uke ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Cheng, X]]
			[[Category: Horton, J R]]
			[[Category: Hydrolase-dna complex]]
			[[Category: Iodine phasing]]
			[[Category: Modification]]
			[[Category: Protein-dna complex]]
			[[Category: Restriction]]

OCA: Protected "6uke" [edit=sysop:move=sysop]

2019-10-16T04:35:39Z

Protected "6uke" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:35, 16 October 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6uke is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2019-10-16T04:35:38Z

New page: '''Unreleased structure''' The entry 6uke is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6uke is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]