1mz8

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Revision as of 12:00, 21 February 2008

CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND A ZINC ION

Overview

H-N-H is a motif found in the nuclease domain of a subfamily of bacteria toxins, including colicin E7, that are capable of cleaving DNA nonspecifically. This H-N-H motif has also been identified in a subfamily of homing endonucleases, which cleave DNA site specifically. To better understand the role of metal ions in the H-N-H motif during DNA hydrolysis, we crystallized the nuclease domain of colicin E7 (nuclease-ColE7) in complex with its inhibitor Im7 in two different crystal forms, and we resolved the structures of EDTA-treated, Zn(2+)-bound and Mn(2+)-bound complexes in the presence of phosphate ions at resolutions of 2.6 A to 2.0 A. This study offers the first determination of the structure of a metal-free and substrate-free enzyme in the H-N-H family. The H-N-H motif contains two antiparallel beta-strands linked to a C-terminal alpha-helix, with a divalent metal ion located in the center. Here we show that the metal-binding sites in the center of the H-N-H motif, for the EDTA-treated and Mg(2+)-soaked complex crystals, were occupied by water molecules, indicating that an alkaline earth metal ion does not reside in the same position as a transition metal ion in the H-N-H motif. However, a Zn(2+) or Mn(2+) ions were observed in the center of the H-N-H motif in cases of Zn(2+) or Mn(2+)-soaked crystals, as confirmed in anomalous difference maps. A phosphate ion was found to bridge between the divalent transition metal ion and His545. Based on these structures and structural comparisons with other nucleases, we suggest a functional role for the divalent transition metal ion in the H-N-H motif in stabilizing the phosphoanion in the transition state during hydrolysis.

About this Structure

1MZ8 is a Protein complex structure of sequences from Escherichia coli with and as ligands. Full crystallographic information is available from OCA.

Reference

Metal ions and phosphate binding in the H-N-H motif: crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions., Sui MJ, Tsai LC, Hsia KC, Doudeva LG, Ku WY, Han GW, Yuan HS, Protein Sci. 2002 Dec;11(12):2947-57. PMID:12441392

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Retrieved from "http://52.214.119.220/wiki/index.php/1mz8"

@@ Line 1: / Line 1: @@
-[[Image:1mz8.gif|left|200px]]<br /><applet load="1mz8" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1mz8.gif|left|200px]]<br /><applet load="1mz8" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1mz8, resolution 2.00&Aring;" />
 '''CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND A ZINC ION'''<br />
 ==Overview==
-H-N-H is a motif found in the nuclease domain of a subfamily of bacteria, toxins, including colicin E7, that are capable of cleaving DNA, nonspecifically. This H-N-H motif has also been identified in a subfamily, of homing endonucleases, which cleave DNA site specifically. To better, understand the role of metal ions in the H-N-H motif during DNA, hydrolysis, we crystallized the nuclease domain of colicin E7, (nuclease-ColE7) in complex with its inhibitor Im7 in two different, crystal forms, and we resolved the structures of EDTA-treated, Zn(2+)-bound and Mn(2+)-bound complexes in the presence of phosphate ions, at resolutions of 2.6 A to 2.0 A. This study offers the first, determination of the structure of a metal-free and substrate-free enzyme, in the H-N-H family. The H-N-H motif contains two antiparallel, beta-strands linked to a C-terminal alpha-helix, with a divalent metal ion, located in the center. Here we show that the metal-binding sites in the, center of the H-N-H motif, for the EDTA-treated and Mg(2+)-soaked complex, crystals, were occupied by water molecules, indicating that an alkaline, earth metal ion does not reside in the same position as a transition metal, ion in the H-N-H motif. However, a Zn(2+) or Mn(2+) ions were observed in, the center of the H-N-H motif in cases of Zn(2+) or Mn(2+)-soaked, crystals, as confirmed in anomalous difference maps. A phosphate ion was, found to bridge between the divalent transition metal ion and His545., Based on these structures and structural comparisons with other nucleases, we suggest a functional role for the divalent transition metal ion in the, H-N-H motif in stabilizing the phosphoanion in the transition state during, hydrolysis.
+H-N-H is a motif found in the nuclease domain of a subfamily of bacteria toxins, including colicin E7, that are capable of cleaving DNA nonspecifically. This H-N-H motif has also been identified in a subfamily of homing endonucleases, which cleave DNA site specifically. To better understand the role of metal ions in the H-N-H motif during DNA hydrolysis, we crystallized the nuclease domain of colicin E7 (nuclease-ColE7) in complex with its inhibitor Im7 in two different crystal forms, and we resolved the structures of EDTA-treated, Zn(2+)-bound and Mn(2+)-bound complexes in the presence of phosphate ions at resolutions of 2.6 A to 2.0 A. This study offers the first determination of the structure of a metal-free and substrate-free enzyme in the H-N-H family. The H-N-H motif contains two antiparallel beta-strands linked to a C-terminal alpha-helix, with a divalent metal ion located in the center. Here we show that the metal-binding sites in the center of the H-N-H motif, for the EDTA-treated and Mg(2+)-soaked complex crystals, were occupied by water molecules, indicating that an alkaline earth metal ion does not reside in the same position as a transition metal ion in the H-N-H motif. However, a Zn(2+) or Mn(2+) ions were observed in the center of the H-N-H motif in cases of Zn(2+) or Mn(2+)-soaked crystals, as confirmed in anomalous difference maps. A phosphate ion was found to bridge between the divalent transition metal ion and His545. Based on these structures and structural comparisons with other nucleases, we suggest a functional role for the divalent transition metal ion in the H-N-H motif in stabilizing the phosphoanion in the transition state during hydrolysis.
 ==About this Structure==
-MZ8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN and PO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MZ8 OCA].
+MZ8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=PO4:'>PO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MZ8 OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Escherichia coli]]
 [[Category: Protein complex]]
-[[Category: Doudeva, L.G.]]
+[[Category: Doudeva, L G.]]
-[[Category: Han, G.W.]]
+[[Category: Han, G W.]]
-[[Category: Hsia, K.C.]]
+[[Category: Hsia, K C.]]
-[[Category: Ku, W.Y.]]
+[[Category: Ku, W Y.]]
-[[Category: Sui, M.J.]]
+[[Category: Sui, M J.]]
-[[Category: Tsai, L.C.]]
+[[Category: Tsai, L C.]]
-[[Category: Yuan, H.S.]]
+[[Category: Yuan, H S.]]
 [[Category: PO4]]
 [[Category: ZN]]
 [[Category: h-n-h motif]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:49:28 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:00:32 2008''

1mz8

From Proteopedia

Revision as of 12:00, 21 February 2008

Overview

About this Structure

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