3M7K

Crystal structure of PacI-DNA Enzyme product complex

Summary for 3M7K

• Entry DOI: 10.2210/pdb3m7k/pdb
• Related: 3LDY
• Descriptor: restriction endonuclease PacI, DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*AP*AP*T)-3'), DNA (5'-D(P*TP*AP*AP*GP*CP*CP*TP*C)-3'), ... (10 entities in total)
• Functional Keywords: hnh restriction endonuclease, beta-beta-alpha-metal active site, 8 base-pair rare cutter, hydrolase-dna complex, hydrolase/dna
• Biological source: Pseudomonas alcaligenes
• Total number of polymer chains: 3
• Total formula weight: 22066.76

Authors

Shen, B.W.,Stoddard, B.L. (deposition date: 2010-03-16, release date: 2010-04-21, Last modification date: 2024-02-21)

Primary citation

Shen, B.W.,Heiter, D.F.,Chan, S.H.,Wang, H.,Xu, S.Y.,Morgan, R.D.,Wilson, G.G.,Stoddard, B.L.
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
Structure, 18:734-743, 2010

PubMed Abstract: The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with its eight-base-pair target recognition sequence 5'-TTAATTAA-3' has been determined to 1.9 A resolution. The enzyme forms an extended homodimer, with each subunit containing two zinc-bound motifs surrounding a betabetaalpha-metal catalytic site. The latter is unusual in that a tyrosine residue likely initiates strand cleavage. PacI dramatically distorts its target sequence from Watson-Crick duplex DNA base pairing, with every base separated from its original partner. Two bases on each strand are unpaired, four are engaged in noncanonical A:A and T:T base pairs, and the remaining two bases are matched with new Watson-Crick partners. This represents a highly unusual DNA binding mechanism for a restriction endonuclease, and implies that initial recognition of the target site might involve significantly different contacts from those visualized in the DNA-bound cocrystal structures.

PubMed: 20541511
DOI: 10.1016/j.str.2010.03.009

Experimental method

X-RAY DIFFRACTION (1.92 Å)