5XZ2

Crystal structure of adenylate kinase

Summary for 5XZ2

• Entry DOI: 10.2210/pdb5xz2/pdb
• Descriptor: Adenylate kinase isoenzyme 1, BIS(ADENOSINE)-5'-PENTAPHOSPHATE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: phosphorylation, transferase
• Biological source: Danio rerio (Zebrafish)
• Total number of polymer chains: 2
• Total formula weight: 45365.02

Authors

Moon, S.,Bae, E.,Kim, J. (deposition date: 2017-07-11, release date: 2018-07-18, Last modification date: 2023-11-22)

Primary citation

Moon, S.,Kim, J.,Bae, E.
Structural analyses of adenylate kinases from Antarctic and tropical fishes for understanding cold adaptation of enzymes
Sci Rep, 7:16027-16027, 2017

PubMed Abstract: Psychrophiles are extremophilic organisms capable of thriving in cold environments. Proteins from these cold-adapted organisms can remain physiologically functional at low temperatures, but are structurally unstable even at moderate temperatures. Here, we report the crystal structure of adenylate kinase (AK) from the Antarctic fish Notothenia coriiceps, and identify the structural basis of cold adaptation by comparison with homologues from tropical fishes including Danio rerio. The structure of N. coriiceps AK (AKNc) revealed suboptimal hydrophobic packing around three Val residues in its central CORE domain, which are replaced with Ile residues in D. rerio AK (AKDr). The Val-to-Ile mutations that improve hydrophobic CORE packing in AKNc increased stability at high temperatures but decreased activity at low temperatures, suggesting that the suboptimal hydrophobic CORE packing is important for cold adaptation. Such linkage between stability and activity was also observed in AKDr. Ile-to-Val mutations that destabilized the tropical AK resulted in increased activity at low temperatures. Our results provide the structural basis of cold adaptation of a psychrophilic enzyme from a multicellular, eukaryotic organism, and highlight the similarities and differences in the structural adjustment of vertebrate and bacterial psychrophilic AKs during cold adaptation.

PubMed: 29167503
DOI: 10.1038/s41598-017-16266-9

Experimental method

X-RAY DIFFRACTION (1.75 Å)