1MZ8

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

Summary for 1MZ8

• Entry DOI: 10.2210/pdb1mz8/pdb
• Related: 7cei
• Descriptor: Colicin E7 immunity protein, Colicin E7, ZINC ION, ... (5 entities in total)
• Functional Keywords: h-n-h motif, toxin, hydrolase-protein binding complex, hydrolase/protein binding
• Biological source: Escherichia coli; More
• Total number of polymer chains: 4
• Total formula weight: 50258.89

Authors

Sui, M.J.,Tsai, L.C.,Hsia, K.C.,Doudeva, L.G.,Ku, W.Y.,Han, G.W.,Yuan, H.S. (deposition date: 2002-10-07, release date: 2002-12-23, Last modification date: 2023-10-25)

Primary citation

Sui, M.J.,Tsai, L.C.,Hsia, K.C.,Doudeva, L.G.,Ku, W.Y.,Han, G.W.,Yuan, H.S.
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
PROTEIN SCI., 11:2947-2957, 2002

PubMed Abstract: 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.

PubMed: 12441392
DOI: 10.1110/ps.0220602

Experimental method

X-RAY DIFFRACTION (2 Å)