4RF9

Crystal structure of double-domain arginine kinase from Anthopleura japonicas in complex with L-arginine and ATPgS

Summary for 4RF9

• Entry DOI: 10.2210/pdb4rf9/pdb
• Related: 4RF6 4RF7 4RF8
• Descriptor: Arginine kinase, ARGININE, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER, ... (5 entities in total)
• Functional Keywords: double domain, tandem domain, phosphagen kinase, transferase
• Biological source: Anthopleura japonica (Sea anemone)
• Total number of polymer chains: 2
• Total formula weight: 161876.41

Authors

Wang, Z.,Qiao, Z.,Ye, S.,Zhang, R. (deposition date: 2014-09-25, release date: 2015-04-08, Last modification date: 2023-09-20)

Primary citation

Wang, Z.,Qiao, Z.,Ye, S.,Zhang, R.
Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.
Acta Crystallogr.,Sect.D, 71:779-789, 2015

PubMed Abstract: Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

PubMed: 25849389
DOI: 10.1107/S1399004715001169

Experimental method

X-RAY DIFFRACTION (2.35 Å)