3sm4 - Revision history

OCA at 13:01, 14 March 2024

OCA — Thu, 14 Mar 2024 13:01:06 GMT

←Older revision		Revision as of 13:01, 14 March 2024
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	<StructureSection load='3sm4' size='340' side='right'caption='[[3sm4]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='3sm4' size='340' side='right'caption='[[3sm4]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sm4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bacteriophage_lambda Bacteriophage lambda~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SM4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sm4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SM4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.88Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3slp\|3slp]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">exo~~, ~~Lambda Exonuclease, red-alpha, redX ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </~~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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [https://pdbe.org/3sm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [https://www.ebi.ac.uk/pdbsum/3sm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sm4 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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [https://pdbe.org/3sm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [https://www.ebi.ac.uk/pdbsum/3sm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sm4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/EXO_LAMBD EXO_LAMBD]] Facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways. Also important for the late, rolling-circle mode of lambda DNA replication.	+	[https://www.uniprot.org/uniprot/EXO_LAMBD EXO_LAMBD] Facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways. Also important for the late, rolling-circle mode of lambda DNA replication.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The lambda exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of lambda exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of lambda exonuclease in complex with DNA at 1.88-A resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg(2+) ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of lambda exonuclease operates not only at the level of the trimer, but also at the level of the monomer.	+
-		+
-	Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity.,Zhang J, McCabe KA, Bell CE Proc Natl Acad Sci U S A. 2011 Jul 5. PMID:21730170<ref>PMID:21730170</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3sm4" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]		*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacteriophage lambda~~]]	+	[[Category: Escherichia virus Lambda]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bell~~, C E~~]]	+	[[Category: Bell CE]]
-	[[Category: Zhang, J]]	+	[[Category: Zhang J]]
-	~~[[Category: 5'-3' dsdna exonuclease]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Homologous recombination]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Recombineering]]~~	+
-	~~[[Category: Single-strand annealing]]~~	+
-	~~[[Category: Type ii restriction endonuclease fold~~]]	+

OCA at 08:01, 29 June 2022

OCA — Wed, 29 Jun 2022 08:01:41 GMT

←Older revision		Revision as of 08:01, 29 June 2022
Line 1:		Line 1:

	==Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium==		==Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium==
-	<StructureSection load='3sm4' size='340' side='right' caption='[[3sm4]], [[Resolution\|resolution]] 1.88Å' scene=''>	+	<StructureSection load='3sm4' size='340' side='right'caption='[[3sm4]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sm4]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3SM4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sm4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SM4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3slp\|3slp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3slp\|3slp]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">exo, Lambda Exonuclease, red-alpha, redX ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">exo, Lambda Exonuclease, red-alpha, redX ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [~~http~~://pdbe.org/3sm4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3sm4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3sm4 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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [https://pdbe.org/3sm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [https://www.ebi.ac.uk/pdbsum/3sm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sm4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/EXO_LAMBD EXO_LAMBD]] Facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways. Also important for the late, rolling-circle mode of lambda DNA replication.	+	[[https://www.uniprot.org/uniprot/EXO_LAMBD EXO_LAMBD]] Facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways. Also important for the late, rolling-circle mode of lambda DNA replication.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3sm4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3sm4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Bacteriophage lambda]]		[[Category: Bacteriophage lambda]]
		+	[[Category: Large Structures]]
	[[Category: Bell, C E]]		[[Category: Bell, C E]]
	[[Category: Zhang, J]]		[[Category: Zhang, J]]

OCA at 09:39, 8 November 2017

OCA — Wed, 08 Nov 2017 09:39:22 GMT

←Older revision		Revision as of 09:39, 8 November 2017
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3sm4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3sm4" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Exonuclease\|Exonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:54, 5 August 2016

OCA — Fri, 05 Aug 2016 05:54:29 GMT

←Older revision		Revision as of 05:54, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium==		==Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium==
	<StructureSection load='3sm4' size='340' side='right' caption='[[3sm4]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='3sm4' size='340' side='right' caption='[[3sm4]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3sm4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_lambda Enterobacteria phage~~ lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SM4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3sm4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SM4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3slp\|3slp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3slp\|3slp]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">exo, Lambda Exonuclease, red-alpha, redX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 ~~Enterobacteria phage~~ lambda])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">exo, Lambda Exonuclease, red-alpha, redX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [http://www.ebi.ac.uk/pdbsum/3sm4 PDBsum]</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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [http://pdbe.org/3sm4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [http://www.ebi.ac.uk/pdbsum/3sm4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sm4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3sm4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 26:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage~~ lambda]]	+	[[Category: Bacteriophage lambda]]
	[[Category: Bell, C E]]		[[Category: Bell, C E]]
	[[Category: Zhang, J]]		[[Category: Zhang, J]]

OCA at 23:34, 24 December 2014

OCA — Wed, 24 Dec 2014 23:34:48 GMT

←Older revision		Revision as of 23:34, 24 December 2014
Line 9:		Line 9:
	<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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [http://www.ebi.ac.uk/pdbsum/3sm4 PDBsum]</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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [http://www.ebi.ac.uk/pdbsum/3sm4 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/EXO_LAMBD EXO_LAMBD]] Facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways. Also important for the late, rolling-circle mode of lambda DNA replication.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 11:31, 9 December 2014

OCA — Tue, 09 Dec 2014 11:31:59 GMT

←Older revision		Revision as of 11:31, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3sm4.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium==
		+	<StructureSection load='3sm4' size='340' side='right' caption='[[3sm4]], [[Resolution\|resolution]] 1.88Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3sm4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SM4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3slp\|3slp]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">exo, Lambda Exonuclease, red-alpha, redX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Enterobacteria phage lambda])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exodeoxyribonuclease_(lambda-induced) Exodeoxyribonuclease (lambda-induced)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.11.3 3.1.11.3] </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=3sm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sm4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sm4 RCSB], [http://www.ebi.ac.uk/pdbsum/3sm4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The lambda exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of lambda exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of lambda exonuclease in complex with DNA at 1.88-A resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg(2+) ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of lambda exonuclease operates not only at the level of the trimer, but also at the level of the monomer.

-	{~~{STRUCTURE_3sm4\| PDB=3sm4 \| SCENE= }~~}	+	Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity.,Zhang J, McCabe KA, Bell CE Proc Natl Acad Sci U S A. 2011 Jul 5. PMID:21730170<ref>PMID:21730170</ref>

-	~~===Crystal Structure~~ of the ~~K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21730170}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3sm4]] is a 5 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA].~~	+

	==See Also==		==See Also==
	*[[Exonuclease\|Exonuclease]]		*[[Exonuclease\|Exonuclease]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021730170<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Enterobacteria phage lambda]]		[[Category: Enterobacteria phage lambda]]
-	[[Category: Bell, C E.]]	+	[[Category: Bell, C E]]
-	[[Category: Zhang, J.]]	+	[[Category: Zhang, J]]
	[[Category: 5'-3' dsdna exonuclease]]		[[Category: 5'-3' dsdna exonuclease]]
	[[Category: Dna repair]]		[[Category: Dna repair]]

OCA at 10:15, 20 October 2012

OCA — Sat, 20 Oct 2012 10:15:46 GMT

←Older revision		Revision as of 10:15, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3sm4]] is a 5 chain structure ~~of [[Exonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA].	+	[[3sm4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA].

	==See Also==		==See Also==

OCA at 01:31, 26 July 2012

OCA — Thu, 26 Jul 2012 01:31:06 GMT

←Older revision		Revision as of 01:31, 26 July 2012
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	[[Image:3sm4.png\|left\|200px]]		[[Image:3sm4.png\|left\|200px]]

-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-	-->
	{{STRUCTURE_3sm4\| PDB=3sm4 \| SCENE= }}		{{STRUCTURE_3sm4\| PDB=3sm4 \| SCENE= }}

	===Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium===		===Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21730170}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21730170 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21730170}}		{{ABSTRACT_PUBMED_21730170}}

	==About this Structure==		==About this Structure==
-	[[3sm4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA].	+	[[3sm4]] is a 5 chain structure of [[Exonuclease]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA].
		+
		+	==See Also==
		+	*[[Exonuclease\|Exonuclease]]

	==Reference==		==Reference==

OCA at 06:16, 27 July 2011

OCA — Wed, 27 Jul 2011 06:16:45 GMT

←Older revision		Revision as of 06:16, 27 July 2011
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-	[[Image:3sm4.~~jpg~~\|left\|200px]]	+	[[Image:3sm4.png\|left\|200px]]

	<!--		<!--

OCA at 06:59, 20 July 2011

OCA — Wed, 20 Jul 2011 06:59:29 GMT

←Older revision		Revision as of 06:59, 20 July 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3sm4.jpg\|left\|200px]]

-	The ~~entry 3sm4~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3sm4", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3sm4\| PDB=3sm4 \| SCENE= }}

-	~~Authors: Bell, C.E., Zhang, J.~~	+	===Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium===

-	~~Description~~: ~~Crystal Structure of~~ the ~~K131A Mutant of Lambda Exonuclease in Complex with~~ a 5'-~~Phosphorylated 14~~-~~mer/12~~-~~mer Duplex and Magnesium~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21730170}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21730170 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21730170}}
		+
		+	==About this Structure==
		+	[[3sm4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SM4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021730170</ref><references group="xtra"/>
		+	[[Category: Enterobacteria phage lambda]]
		+	[[Category: Bell, C E.]]
		+	[[Category: Zhang, J.]]
		+	[[Category: 5'-3' dsdna exonuclease]]
		+	[[Category: Dna repair]]
		+	[[Category: Homologous recombination]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Recombineering]]
		+	[[Category: Single-strand annealing]]
		+	[[Category: Type ii restriction endonuclease fold]]