3L0S

Crystal structures of Zinc, Cobalt and Iron containing Adenylate kinase from Gram-negative bacteria Desulfovibrio gigas

Summary for 3L0S

• Entry DOI: 10.2210/pdb3l0s/pdb
• Descriptor: Adenylate kinase, COBALT (II) ION, D(-)-TARTARIC ACID, ... (4 entities in total)
• Functional Keywords: adenylate kinase, gram-negative, cobalt, atp-binding, kinase, nucleotide-binding, transferase
• Biological source: Desulfovibrio gigas
• Cellular location: Cytoplasm (By similarity): C7U112
• Total number of polymer chains: 2
• Total formula weight: 49508.01

Authors

Mukhopadhyay, A.,Trincao, J.,Romao, M.J. (deposition date: 2009-12-10, release date: 2010-12-15, Last modification date: 2024-03-20)

Primary citation

Mukhopadhyay, A.,Kladova, A.V.,Bursakov, S.A.,Gavel, O.Y.,Calvete, J.J.,Shnyrov, V.L.,Moura, I.,Moura, J.J.G.,Romao, M.J.,Trincao, J.
Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria
J.Biol.Inorg.Chem., 16:51-61, 2011

PubMed Abstract: Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, 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 (Zn(2+), Zn-AK; Co(2+), Co-AK; and Fe(2+), Fe-AK) bound in its LID domain have been determined by X-ray crystallography to resolutions 1.8, 2.0, and 3.0 Å, respectively. The zinc and iron forms of the enzyme were crystallized in space group I222, whereas the cobalt-form crystals were C2. The presence of the metals was confirmed by calculation of anomalous difference maps and by X-ray fluorescence scans. The work presented here is the first report of a structure of a metal-containing AK from a Gram-negative bacterium. The native enzyme was crystallized, and only zinc was detected in the LID domain. Co-AK and Fe-AK were obtained by overexpressing the protein in Escherichia coli. Zn-AK and Fe-AK crystallized as monomers in the asymmetric unit, whereas Co-AK crystallized as a dimer. Nevertheless, 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. In the absence of any substrate, the LID domain of all holoforms of AK was present in a fully open conformational state. Normal mode analysis was performed to predict fluctuations of the LID domain along the catalytic pathway.

PubMed: 20821240
DOI: 10.1007/s00775-010-0700-8

Experimental method

X-RAY DIFFRACTION (2 Å)