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1mz8
From Proteopedia
(New page: 200px<br /><applet load="1mz8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mz8, resolution 2.00Å" /> '''CRYSTAL STRUCTURES O...) |
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| - | [[Image:1mz8.gif|left|200px]]<br /><applet load="1mz8" size=" | + | [[Image:1mz8.gif|left|200px]]<br /><applet load="1mz8" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1mz8, resolution 2.00Å" /> | caption="1mz8, resolution 2.00Å" /> | ||
'''CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND A ZINC ION'''<br /> | '''CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND A ZINC ION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | H-N-H is a motif found in the nuclease domain of a subfamily of bacteria | + | 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== | ==About this Structure== | ||
| - | 1MZ8 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:// | + | 1MZ8 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== | ==Reference== | ||
| Line 13: | Line 13: | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Doudeva, L | + | [[Category: Doudeva, L G.]] |
| - | [[Category: Han, G | + | [[Category: Han, G W.]] |
| - | [[Category: Hsia, K | + | [[Category: Hsia, K C.]] |
| - | [[Category: Ku, W | + | [[Category: Ku, W Y.]] |
| - | [[Category: Sui, M | + | [[Category: Sui, M J.]] |
| - | [[Category: Tsai, L | + | [[Category: Tsai, L C.]] |
| - | [[Category: Yuan, H | + | [[Category: Yuan, H S.]] |
[[Category: PO4]] | [[Category: PO4]] | ||
[[Category: ZN]] | [[Category: ZN]] | ||
[[Category: h-n-h motif]] | [[Category: h-n-h motif]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:00:32 2008'' |
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
Page seeded by OCA on Thu Feb 21 14:00:32 2008
Categories: Escherichia coli | Protein complex | Doudeva, L G. | Han, G W. | Hsia, K C. | Ku, W Y. | Sui, M J. | Tsai, L C. | Yuan, H S. | PO4 | ZN | H-n-h motif
