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==Crystal structure of lambda exonuclease in complex with DNA and Ca2+==
==Crystal structure of lambda exonuclease in complex with DNA and Ca2+==
<StructureSection load='4wuz' size='340' side='right' caption='[[4wuz]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
<StructureSection load='4wuz' size='340' side='right'caption='[[4wuz]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4wuz]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WUZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WUZ FirstGlance]. <br>
<table><tr><td colspan='2'>[[4wuz]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WUZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WUZ FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.38&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4wuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wuz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wuz RCSB], [http://www.ebi.ac.uk/pdbsum/4wuz PDBsum]</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=4wuz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wuz OCA], [https://pdbe.org/4wuz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wuz RCSB], [https://www.ebi.ac.uk/pdbsum/4wuz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wuz ProSAT]</span></td></tr>
</table>
</table>
== 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.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bacteriophage lambda exonuclease (lambdaexo) is a ring-shaped homotrimer that resects double-stranded DNA ends in the 5'-3' direction to generate a long 3'-overhang that is a substrate for recombination. lambdaexo is a member of the type II restriction endonuclease-like superfamily of proteins that use a Mg2+-dependent mechanism for nucleotide cleavage. A previous structure of lambdaexo in complex with DNA and Mg2+ was determined using a nuclease defective K131A variant to trap a stable complex. This structure revealed the detailed coordination of the two active site Mg2+ ions but did not show the interactions involving the side chain of the conserved active site Lys-131 residue. Here, we have determined the crystal structure of wild-type (WT) lambdaexo in complex with the same DNA substrate, but in the presence of Ca2+ instead of Mg2+. Surprisingly, there is only one Ca2+ bound in the active site, near the position of MgA in the structure with Mg2+. The scissile phosphate is displaced by 2.2 A relative to its position in the structure with Mg2+, and the network of interactions involving the attacking water molecule is broken. Thus, the structure does not represent a catalytic configuration. However, the crystal structure does show clear electron density for the side chain of Lys-131, which is held in place by interactions with Gln-157 and Glu-129. By combining the K131A-Mg2+ and WT-Ca2+ structures, we constructed a composite model to show the likely interactions of Lys-131 during catalysis. The implications with regard to the catalytic mechanism are discussed.
Crystal Structure of lambda Exonuclease in Complex with DNA and Ca,Zhang J, Pan X, Bell CE Biochemistry. 2014 Nov 19. PMID:25370446<ref>PMID:25370446</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4wuz" style="background-color:#fffaf0;"></div>
==See Also==
*[[Exonuclease 3D structures|Exonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bell, C E]]
[[Category: Escherichia virus Lambda]]
[[Category: Zhang, J]]
[[Category: Large Structures]]
[[Category: Exonuclease]]
[[Category: Synthetic construct]]
[[Category: Type ii restriction endonuclease]]
[[Category: Bell CE]]
[[Category: Zhang J]]
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