1RL9

Crystal structure of Creatine-ADP arginine kinase ternary complex

Summary for 1RL9

• Entry DOI: 10.2210/pdb1rl9/pdb
• Related: 1BGO
• Descriptor: Arginine kinase, MAGNESIUM ION, ADENOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: arginine kinase, transferase
• Biological source: Limulus polyphemus (Atlantic horseshoe crab)
• Cellular location: Cytoplasm: P51541
• Total number of polymer chains: 1
• Total formula weight: 40893.43

Authors

Azzi, A.,Clark, S.A.,Ellington, R.W.,Chapman, M.S. (deposition date: 2003-11-25, release date: 2004-05-25, Last modification date: 2023-08-23)

Primary citation

Azzi, A.,Clark, S.A.,Ellington, W.R.,Chapman, M.S.
The role of phosphagen specificity loops in arginine kinase.
Protein Sci., 13:575-585, 2004

PubMed Abstract: Phosphagen kinases catalyze the reversible transfer of a phosphate between ATP and guanidino substrates, a reaction that is central to cellular energy homeostasis. Members of this conserved family include creatine and arginine kinases and have similar reaction mechanisms, but they have distinct specificities for different guanidino substrates. There has not been a full structural rationalization of specificity, but two loops have been implicated repeatedly. A small domain loop is of length that complements the size of the guanidino substrate, and is located where it could mediate a lock-and-key mechanism. The second loop contacts the substrate with a valine in the methyl-substituted guanidinium of creatine, and with a glutamate in the unsubstituted arginine substrate, leading to the proposal of a discriminating hydrophobic/hydrophilic minipocket. In the present work, chimeric mutants were constructed with creatine kinase loop elements inserted into arginine kinase. Contrary to the prior rationalizations of specificity, most had measurable arginine kinase activity but no creatine kinase activity or enhanced phosphocreatine binding. Guided by structure, additional mutations were introduced in each loop, recovering arginine kinase activities as high as 15% and 64% of wild type, respectively, even though little activity would be expected in the constructs if the implicated sites had dominant roles in specificity. An atomic structure of the mismatched complex of arginine kinase with creatine and ADP indicates that specificity can also be mediated by an active site that allows substrate prealignment that is optimal for reactivity only with cognate substrates and not with close homologs that bind but do not react.

PubMed: 14978299
DOI: 10.1110/ps.03428304

Experimental method

X-RAY DIFFRACTION (1.45 Å)