ArticleProtein science : a publication of the Protein Society2006
Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+.
Article in Protein science : a publication of the Protein Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 47 citations in OpenAlex.
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- Molecular Structure and Functional Analysis of Pyocin S8 from Pseudomonas aeruginosa Reveals the Essential Requirement of a Glutamate Residue in the H-N-H Motif for DNase Activity.Journal of bacteriology · 2020Article
- HK97 gp74 Possesses an α-Helical Insertion in the ββα Fold That Affects Its Metal Binding,Journal of bacteriology · 2020Article
- A comparison of computational methodologies for the structural modelling of biologically relevant zinc complexes.Journal of molecular modeling · 2019Article
- Crystal structure of NucB, a biofilm-degrading endonuclease.Nucleic acids research · 2018Article
- Structural and functional characterization of deep-sea thermophilic bacteriophage GVE2 HNH endonuclease.Scientific reports · 2017Article
- Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study.Protein science : a publication of the Protein Society · 2016Article
- Substrate binding activates the designed triple mutant of the colicin E7 metallonuclease.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2014Article
- Fine tuning of the catalytic activity of colicin E7 nuclease domain by systematic N-terminal mutations.Protein science : a publication of the Protein Society · 2014Article
- Design of a colicin E7 based chimeric zinc-finger nuclease.Journal of computer-aided molecular design · 2014Article
- Crystallization and preliminary crystallographic analysis of an Escherichia coli-selected mutant of the nuclease domain of the metallonuclease colicin E7.Acta crystallographica. Section F, Structural biology and crystallization communications · 2013Article
- The role of the N-terminal loop in the function of the colicin E7 nuclease domain.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2013Article
- Bacillus subtilis hlpB encodes a conserved stand-alone HNH nuclease-like protein that is essential for viability unless the hlpB deletion is accompanied by the deletion of genes encoding the AddAB DNA repair complex.Journal of bacteriology · 2012Article
- Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA.The Journal of biological chemistry · 2011Article
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8 authors at 3 institutions in 1 country.
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Abstract
The nuclease domain of ColE7 (N-ColE7) contains an H-N-H motif that folds in a beta beta alpha-metal topology. Here we report the crystal structures of a Zn2+-bound N-ColE7 (H545E mutant) in complex with a 12-bp duplex DNA and a Ni2+-bound N-ColE7 in complex with the inhibitor Im7 at a resolution of 2.5 A and 2.0 A, respectively. Metal-dependent cleavage assays showed that N-ColE7 cleaves double-stranded DNA with a single metal ion cofactor, Ni2+, Mg2+, Mn2+, and Zn2+. ColE7 purified from Escherichia coli contains an endogenous zinc ion that was not replaced by Mg2+ at concentrations of <25 mM, indicating that zinc is the physiologically relevant metal ion in N-ColE7 in host E. coli. In the crystal structure of N-ColE7/DNA complex, the zinc ion is directly coordinated to three histidines and the DNA scissile phosphate in a tetrahedral geometry. In contrast, Ni2+ is bound in N-ColE7 in two different modes, to four ligands (three histidines and one phosphate ion), or to five ligands with an additional water molecule. These data suggest that the divalent metal ion in the His-metal finger motif can be coordinated to six ligands, such as Mg2+ in I-PpoI, Serratia nuclease and Vvn, five ligands or four ligands, such as Ni2+ or Zn2+ in ColE7. Universally, the metal ion in the His-metal finger motif is bound to the DNA scissile phosphate and serves three roles during hydrolysis: polarization of the P-O bond for nucleophilic attack, stabilization of the phosphoanion transition state and stabilization of the cleaved product.
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