Induced fit in guanidino kinases—comparison of substrate‐free and transition state analog structures of arginine kinase

• Published in: Protein science 2003-01, Vol.12 (1), p.103-111
• Main Authors: Yousef, Mohammad S., Clark, Shawn A., Pruett, Pamela K., Somasundaram, Thayumanasamy, Ellington, W. Ross, Chapman, Michael S.
• Format: Article
• Language: English
• Subjects: Adenosine Diphosphate - metabolism; Animals; arginine kinase; Arginine Kinase - chemistry; Arginine Kinase - genetics; Arginine Kinase - metabolism; Binding Sites; Cloning, Molecular; creatine kinase; Creatine Kinase - chemistry; Crystallography, X-Ray; Guanidines; guanidino kinase; Horseshoe Crabs - enzymology; Humans; Induced fit; Models, Molecular; Protein Conformation; Protein Structure, Tertiary; structure; Structure-Activity Relationship; Substrate Specificity
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1110/ps.0226303

Arginine kinase (AK) is a member of the guanidino kinase family that plays an important role in buffering ATP concentration in cells with high and fluctuating energy demands. The AK specifically catalyzes the reversible phosphoryl transfer between ATP and arginine. We have determined the crystal structure of AK from the horseshoe crab (Limulus polyphemus) in its open (substrate‐free) form. The final model has been refined at 2.35 Å with a final R of 22.3% (Rfree = 23.7%). The structure of the open form is compared to the previously determined structure of the transition state analog complex in the closed form. Classically, the protein would be considered two domain, but dynamic domain (DynDom) analysis shows that most of the differences between the two structures can be considered as the motion between four rigid groups of nonsequential residues. ATP binds near a cluster of positively charged residues of a fixed dynamic domain. The other three dynamic domains close the active site with separate hinge rotations relative to the fixed domain. Several residues of key importance for the induced motion are conserved within the phosphagen kinase family, including creatine kinase. Substantial conformational changes are induced in different parts of the enzyme as intimate interactions are formed with both substrates. Thus, although induced fit occurs in a number of phosphoryl transfer enzymes, the conformational changes in phosphagen kinases appear to be more complicated than in prior examples.