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Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap 5 A, Mg 2+ Ap 5 A, and Mn 2+ Ap 5 A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg 2+ and Mn 2+
Author(s) -
Berry Michael B.,
Phillips George N.
Publication year - 1998
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19980815)32:3<276::aid-prot3>3.0.co;2-g
Subject(s) - position (finance) , adenylate kinase , crystal (programming language) , chemistry , crystallography , geometry , physics , nuclear magnetic resonance , mathematics , enzyme , finance , computer science , programming language , economics
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap 5 A, Mn 2+ Ap 5 A, and Mg 2+ Ap 5 A have been determined by X‐ray crystallography to resolutions of 1.6 Å, 1.85 Å, and 1.96 Å, respectively. The protein's lid domain is partially open, being both rotated and translated away from bound Ap 5 A. The flexibility of the lid domain in the ternary state and its ability to transfer force directly to the the active site is discussed in light of our proposed entropic mechanism for catalytic turnover. The bound Zn 2+ atom is demonstrably structural in nature, with no contacts other than its ligating cysteine residues within 5 Å. The B. stearothermophilus adenylate kinase lid appears to be a truncated zinc finger domain, lacking the DNA binding finger, which we have termed a zinc knuckle domain. In the Mg 2+ Ap 5 A and Mn 2+ Ap 5 A structures, Mg 2+ and Mn 2+ demonstrate six coordinate octahedral geometry. The interactions of the Mg 2+ ‐coordinated water molecules with the protein and Ap 5 A phosphate chain demonstrate their involvement in catalyzing phosphate transfer. The protein selects for β‐γ (preferred by Mg 2+ ) rather than α‐γ (preferred by Mn 2+ ) metal ion coordination by forcing the ATP phosphate chain to have an extended conformation. Proteins 32:276–288, 1998. © 1998 Wiley‐Liss, Inc.