4wuz | pdb_00004wuz

Crystal structure of lambda exonuclease in complex with DNA and Ca2+

spinqualitylabelsall models 4wuz, resolution 2.38Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4wuz is a 5 chain structure with sequence from Escherichia virus Lambda and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, PO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Exonuclease 3D structures

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