Crystal structure of the zinc, cobalt and iron containing adenylate kinase from Desulfovibrio gigas: a novel metal containing adenylate kinase from Gram-negative bacteria
A. Mukhopadhyay, A.V. Kladova, S.A. Bursakov, O. Yu. Gavel, J.J. Calvete, V.L. Shnyrov, I. Moura, J.J.G. Moura, M.J. Romão, J. Trincão
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Molecular Tour
Adenylate kinase (ATP:AMP phosphotransferase, EC 2.7.4.3; AK) is an essential catalyst for cellular growth and multiplication. AK belongs to a family of enzymes essential to life, and is highly abundant inside the cell. It is involved in the reversible transfer of the terminal phosphate group from Mg2+ATP to Mg2+AMP with high energy turnover: Mg2+ATP + AMP↔Mg2+ADP + ADP.
Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, , zinc, cobalt and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions: (2xb4); (3l0s) and (3l0p) bound in its LID domain have been determined by X-ray crystallography. All three crystal structures are very similar to each other with the same LID domain topology, the only change being the presence of the different metal atoms.
The structures of Zn- , Co- and Fe-AK contain the and , which also include the AMP binding region. The LID domain harbors the , which is responsible for metal binding in a tetrahedral fashion. In the absence of any substrate, the LID domain of all holo forms of AK was present in a fully open conformational state. The Core domain is . This Core domain mainly consists of a that keep the integrity of the tertiary structure of the enzyme. A with conserved sequence; G-X-X-G-X-G-K is present in the N-terminal region. The structures presented herein further reinforce the notion that the metal ion is purely structural, contributing to the stability of the LID domain.
