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Structural basis for a reciprocating mechanism of negative cooperativity in dimeric phosphagen kinase activity.

Wu X, Ye S, Guo S, Yan W, Bartlam M, Rao Z
FASEB J 24 242-52 (2010)
Cited: 22 times
EuropePMC logo PMID: 19783784

Abstract

Phosphagen kinase (PK) family members catalyze the reversible phosphoryl transfer between phosphagen and ADP to reserve or release energy in cell energy metabolism. The structures of classic quaternary complexes of dimeric creatine kinase (CK) revealed asymmetric ligand binding states of two protomers, but the significance and mechanism remain unclear. To understand this negative cooperativity further, we determined the first structure of dimeric arginine kinase (dAK), another PK family member, at 1.75 A, as well as the structure of its ternary complex with AMPPNP and arginine. Further structural analysis shows that the ligand-free protomer in a ligand-bound dimer opens more widely than the protomers in a ligand-free dimer, which leads to three different states of a dAK protomer. The unexpected allostery of the ligand-free protomer in a ligand-bound dimer should be relayed from the ligand-binding-induced allostery of its adjacent protomer. Mutations that weaken the interprotomer connections dramatically reduced the catalytic activities of dAK, indicating the importance of the allosteric propagation mediated by the homodimer interface. These results suggest a reciprocating mechanism of dimeric PK, which is shared by other ATP related oligomeric enzymes, e.g., ATP synthase.

Articles - 3ju6 mentioned but not cited (3)

  1. The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. Xu Q, Dunbrack RL. Nucleic Acids Res 39 D761-70 (2011)
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  3. Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication. Guarnera E, Berezovsky IN. PLoS Comput Biol 12 e1004678 (2016)


Reviews citing this publication (1)

  1. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Petkowski JJ, Bains W, Seager S. Molecules 24 E866 (2019)

Articles citing this publication (18)

  1. Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response. Tee WV, Guarnera E, Berezovsky IN. PLoS Comput Biol 14 e1006228 (2018)
  2. Crystal structure of shrimp arginine kinase in binary complex with arginine-a molecular view of the phosphagen precursor binding to the enzyme. López-Zavala AA, García-Orozco KD, Carrasco-Miranda JS, Sugich-Miranda R, Velázquez-Contreras EF, Criscitiello MF, Brieba LG, Rudiño-Piñera E, Sotelo-Mundo RR. J Bioenerg Biomembr 45 511-518 (2013)
  3. The structure of lombricine kinase: implications for phosphagen kinase conformational changes. Bush DJ, Kirillova O, Clark SA, Davulcu O, Fabiola F, Xie Q, Somasundaram T, Ellington WR, Chapman MS. J Biol Chem 286 9338-9350 (2011)
  4. Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs. Clark SA, Davulcu O, Chapman MS. Biochem Biophys Res Commun 427 212-217 (2012)
  5. The Michaelis Complex of Arginine Kinase Samples the Transition State at a Frequency That Matches the Catalytic Rate. Peng Y, Hansen AL, Bruschweiler-Li L, Davulcu O, Skalicky JJ, Chapman MS, Brüschweiler R. J Am Chem Soc 139 4846-4853 (2017)
  6. Characterization of a putative oomycete taurocyamine kinase: Implications for the evolution of the phosphagen kinase family. Palmer A, Begres BN, Van Houten JM, Snider MJ, Fraga D. Comp Biochem Physiol B Biochem Mol Biol 166 173-181 (2013)
  7. Cold-adapted features of arginine kinase from the deep-sea clam Calyptogena kaikoi. Suzuki T, Yamamoto K, Tada H, Uda K. Mar Biotechnol (NY) 14 294-303 (2012)
  8. Impact of inter-subunit interactions on the dimeric arginine kinase activity and structural stability. Wu QY, Li F, Wang XY, Chen ZJ. Arch Biochem Biophys 512 61-68 (2011)
  9. Impact of intra-subunit interactions on the dimeric arginine kinase activity and structural stability. Wu QY, Jin KZ, Li F, Hu ZQ, Wang XY. Int J Biol Macromol 49 822-831 (2011)
  10. Arginine kinases from the marine feather star Tropiometra afra macrodiscus: The first finding of a prenylation signal sequence in metazoan phosphagen kinases. Chouno K, Yano D, Uda K, Fujita T, Iwasaki N, Suzuki T. Comp Biochem Physiol B Biochem Mol Biol 187 55-61 (2015)
  11. Cooperativity and evolution of Tetrahymena two-domain arginine kinase. Okazaki N, Motomura S, Okazoe N, Yano D, Suzuki T. Int J Biol Macromol 79 696-703 (2015)
  12. Mutation of residue arginine 330 of arginine kinase results in the generation of the oxidized form more susceptible. Wang WD, Wang JS, Shi YL, Zhang XC, Pan JC, Zou GL. Int J Biol Macromol 54 238-243 (2013)
  13. The D14 and R138 ion pair is involved in dimeric arginine kinase activity, structural stability and folding. Geng HL, Bian MR, Liu Y, Cao J, Chen C, Wang ZY, Li ZY, Zeng LY, Wang XY, Wu QY, Xu KL. Int J Biol Macromol 66 302-310 (2014)
  14. The substrate-free and -bound crystal structures of the duplicated taurocyamine kinase from the human parasite Schistosoma mansoni. Merceron R, Awama AM, Montserret R, Marcillat O, Gouet P. J Biol Chem 290 12951-12963 (2015)
  15. Arginine kinase shows nucleoside diphosphate kinase-like activity toward deoxythymidine diphosphate. Lopez-Zavala AA, Sotelo-Mundo RR, Hernandez-Flores JM, Lugo-Sanchez ME, Sugich-Miranda R, Garcia-Orozco KD. J Bioenerg Biomembr 48 301-308 (2016)
  16. Dynamical properties of the loop 320s of substrate-free and substrate-bound muscle creatine kinase by NMR: evidence for independent subunits. Rivière G, Hologne M, Marcillat O, Lancelin JM. FEBS J 279 2863-2875 (2012)
  17. Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains. Wang Z, Qiao Z, Ye S, Zhang R. Acta Crystallogr D Biol Crystallogr 71 779-789 (2015)
  18. Crystal Structure of H227A Mutant of Arginine Kinase in Daphnia magna Suggests the Importance of Its Stability. Kim DS, Jang K, Kim WS, Ryu M, Park JH, Kim YJ. Molecules 27 884 (2022)


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