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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^[1]

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