3sm4 | pdb_00003sm4

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

spinqualitylabelsall models 3sm4, resolution 1.88Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3sm4 is a 5 chain structure with sequence from Enterobacteria phage lambda. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CL, MG, PO4 Related: 3slp Gene: exo, Lambda Exonuclease, red-alpha, redX (Enterobacteria phage lambda) Activity: Exodeoxyribonuclease (lambda-induced), with EC number 3.1.11.3 Resources: FirstGlance, OCA, RCSB, PDBsum 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Exonuclease

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