PDBsum entry 1fiu

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Hydrolase/DNA PDB id
Protein chains
286 a.a.
ACY ×4
_MG ×8
Waters ×1279

References listed in PDB file
Key reference
Title Structure of the tetrameric restriction endonuclease ngomiv in complex with cleaved DNA.
Authors M.Deibert, S.Grazulis, G.Sasnauskas, V.Siksnys, R.Huber.
Ref. Nat Struct Biol, 2000, 7, 792-799. [DOI no: 10.1038/79032]
PubMed id 10966652
The crystal structure of the NgoMIV restriction endonuclease in complex with cleaved DNA has been determined at 1.6 A resolution. The crystallographic asymmetric unit contains a protein tetramer and two DNA molecules cleaved at their recognition sites. This is the first structure of a tetrameric restriction enzyme-DNA complex. In the tetramer, two primary dimers are arranged back to back with two oligonucleotides bound in clefts on opposite sides of the tetramer. The DNA molecules retain a B-type conformation and have an enclosed angle between their helical axes of 60 degrees. Sequence-specific interactions occur in both the major and minor grooves. Two Mg2+ ions are located close to the cleaved phosphate at the active site of NgoMIV. Biochemical experiments show that interactions between the recognition sites within the tetramer greatly increase DNA cleavage efficiency.
Figure 1.
Figure 1. Overall structure of the NgoMIV -DNA complex. a, Side view of the NgoMIV -DNA complex. Monomers are colored blue (A), red (B), green (C) and gray (D). DNA is shown in yellow and Mg2+ ions as magenta spheres. b, View of the NgoMIV -DNA complex along the axis of one DNA duplex. c, NgoMIV monomer with labeled -helices and 3[10]-helices and -strands. The chain runs from blue (N-terminus, N) to red (C-terminus, C). d, Topology diagram of NgoMIV. The central -sheet is shown in blue, protruding arms in green, and recognition helices in red.
Figure 3.
Figure 3. The active site of NgoMIV. a, Stereo view of the coordination geometry of Mg2+ ions at the active site of NgoMIV in the enzyme -product complex. Two Mg2+ ions are shown as green spheres. Both Mg2+ exhibit octahedral coordination. The O2P of the 5' phosphate, the carboxylate of Asp 140 and the acetate molecule contribute to the coordination of both Mg2+ ions. The remaining three ligands of Mg 2+ ion A are the backbone oxygen of Cys 186 and water molecules 1 and 2 (shown as blue spheres). Water molecules 3 -5 complete the octahedral coordination of Mg2+ ion B. All Mg coordinated waters are fixed by either protein and/or DNA residues. The final 2F[o] - F[ c] electron density for the DNA is shown contoured at 1.5 . b, Stereo view of the superimposed active sites of NgoMIV and Cfr10I. The Cfr10I residues are shown in blue, the NgoMIV residues in green, with the two Mg2+ ions shown as green spheres. c, Stereo view of the superimposed active sites of BamHI and NgoMIV. The BamHI residues are shown in magenta, the NgoMIV residues in green with the two metal ions as magenta (Mn2+ in BamHI) and green (Mg2+ in NgoMIV) spheres. Note that four acidic residues (Glu 77, Asp 94, Glu 111 and Glu 113) are located in the vicinity of the Mn2+ ions at the active site of BamHI, while only three (Glu 70, Asp 140, Glu 201) are present at the active site of NgoMIV. Lys 187 of NgoMIV is structurally equivalent to Glu 113 of BamHI.
The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 792-799) copyright 2000.
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