1zns: Difference between revisions
New page: left|200px<br /><applet load="1zns" size="450" color="white" frame="true" align="right" spinBox="true" caption="1zns, resolution 2.50Å" /> '''Crystal structure of... |
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[[Image:1zns.gif|left|200px]]<br /><applet load="1zns" size=" | [[Image:1zns.gif|left|200px]]<br /><applet load="1zns" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1zns, resolution 2.50Å" /> | caption="1zns, resolution 2.50Å" /> | ||
'''Crystal structure of N-ColE7/12-bp DNA/Zn complex'''<br /> | '''Crystal structure of N-ColE7/12-bp DNA/Zn complex'''<br /> | ||
==Overview== | ==Overview== | ||
The nuclease domain of ColE7 (N-ColE7) contains an H-N-H motif that folds | 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. | ||
==About this Structure== | ==About this Structure== | ||
1ZNS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | 1ZNS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZNS OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Doudeva, L | [[Category: Doudeva, L G.]] | ||
[[Category: Hsia, K | [[Category: Hsia, K C.]] | ||
[[Category: Huang, H.]] | [[Category: Huang, H.]] | ||
[[Category: Li, C | [[Category: Li, C L.]] | ||
[[Category: Shen, Y.]] | [[Category: Shen, Y.]] | ||
[[Category: Shi, Z.]] | [[Category: Shi, Z.]] | ||
[[Category: Yuan, H | [[Category: Yuan, H S.]] | ||
[[Category: ZN]] | [[Category: ZN]] | ||
[[Category: colicin]] | [[Category: colicin]] | ||
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[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:17:33 2008'' | ||
Revision as of 17:17, 21 February 2008
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Crystal structure of N-ColE7/12-bp DNA/Zn complex
OverviewOverview
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.
About this StructureAbout this Structure
1ZNS is a Single protein structure of sequence from Escherichia coli with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+., Doudeva LG, Huang H, Hsia KC, Shi Z, Li CL, Shen Y, Cheng YS, Yuan HS, Protein Sci. 2006 Feb;15(2):269-80. PMID:16434744
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