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Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase.

Hible G, Renault L, Schaeffer F, Christova P, Zoe Radulescu A, Evrin C, Gilles AM, Cherfils J
J Mol Biol 352 1044-59 (2005)
Related entries: 2an9, 2anb

Cited: 19 times
EuropePMC logo PMID: 16140325

Abstract

Guanosine monophosphate kinases (GMPKs), which catalyze the phosphorylation of GMP and dGMP to their diphosphate form, have been characterized as monomeric enzymes in eukaryotes and prokaryotes. Here, we report that GMPK from Escherichia coli (ecGMPK) assembles in solution and in the crystal as several different oligomers. Thermodynamic analysis of ecGMPK using differential scanning calorimetry shows that the enzyme is in equilibrium between a dimer and higher order oligomers, whose relative amounts depend on protein concentration, ionic strength, and the presence of ATP. Crystallographic structures of ecGMPK in the apo, GMP and GDP-bound forms were solved at 3.2A, 2.9A and 2.4A resolution, respectively. ecGMPK forms a hexamer with D3 symmetry in all crystal forms, in which the two nucleotide-binding domains are able to undergo closure comparable to that of monomeric GMPKs. The 2-fold and 3-fold interfaces involve a 20-residue C-terminal extension and a sequence signature, respectively, that are missing from monomeric eukaryotic GMPKs, explaining why ecGMPK forms oligomers. These signatures are found in GMPKs from proteobacteria, some of which are human pathogens. GMPKs from these bacteria are thus likely to form the same quaternary structures. The shift of the thermodynamic equilibrium towards the dimer at low ecGMPK concentration together with the observation that inter-subunit interactions partially occlude the ATP-binding site in the hexameric structure suggest that the dimer may be the active species at physiological enzyme concentration.

Reviews - 2anc mentioned but not cited (1)

  1. Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies. Olenginski LT, Taiwo KM, LeBlanc RM, Dayie TK. Molecules 26 5581 (2021)

Articles - 2anc mentioned but not cited (1)

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Articles citing this publication (17)

  1. Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Russell RB, Heck AJ, Bork P, Gavin AC. Mol Syst Biol 8 571 (2012)
  2. Proteins evolve on the edge of supramolecular self-assembly. Garcia-Seisdedos H, Empereur-Mot C, Elad N, Levy ED. Nature 548 244-247 (2017)
  3. Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains. Akiva E, Itzhaki Z, Margalit H. Proc Natl Acad Sci U S A 105 13292-13297 (2008)
  4. Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp. Liu K, Myers AR, Pisithkul T, Claas KR, Satyshur KA, Amador-Noguez D, Keck JL, Wang JD. Mol Cell 57 735-749 (2015)
  5. Substrate-induced conformational changes in the essential peripheral membrane-associated mannosyltransferase PimA from mycobacteria: implications for catalysis. Guerin ME, Schaeffer F, Chaffotte A, Gest P, Giganti D, Korduláková J, van der Woerd M, Jackson M, Alzari PM. J Biol Chem 284 21613-21625 (2009)
  6. Complex molecular assemblies at hand via interactive simulations. Delalande O, Férey N, Grasseau G, Baaden M. J Comput Chem 30 2375-2387 (2009)
  7. Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase. Hible G, Christova P, Renault L, Seclaman E, Thompson A, Girard E, Munier-Lehmann H, Cherfils J. Proteins 62 489-500 (2006)
  8. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis. Pisithkul T, Jacobson TB, O'Brien TJ, Stevenson DM, Amador-Noguez D. Appl Environ Microbiol 81 5761-5772 (2015)
  9. Crystal structures of GMP kinase in complex with ganciclovir monophosphate and Ap5G. Hible G, Daalova P, Gilles AM, Cherfils J. Biochimie 88 1157-1164 (2006)
  10. Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase. Ofiteru A, Bucurenci N, Alexov E, Bertrand T, Briozzo P, Munier-Lehmann H, Gilles AM. FEBS J 274 3363-3373 (2007)
  11. Molecular cloning, expression, characterization and mutation of Plasmodium falciparum guanylate kinase. Kandeel M, Nakanishi M, Ando T, El-Shazly K, Yosef T, Ueno Y, Kitade Y. Mol Biochem Parasitol 159 130-133 (2008)
  12. Functional versatility of a single protein surface in two protein:protein interactions. Adikaram PR, Beckett D. J Mol Biol 419 223-233 (2012)
  13. Solution structure and functional investigation of human guanylate kinase reveals allosteric networking and a crucial role for the enzyme in cancer. Khan N, Shah PP, Ban D, Trigo-Mouriño P, Carneiro MG, DeLeeuw L, Dean WL, Trent JO, Beverly LJ, Konrad M, Lee D, Sabo TM. J Biol Chem 294 11920-11933 (2019)
  14. Search for proteins required for accurate gene expression under oxidative stress: roles of guanylate kinase and RNA polymerase. Inokuchi H, Ito R, Sekiguchi T, Sekiguchi M. J Biol Chem 288 32952-32962 (2013)
  15. Enzyme closure and nucleotide binding structurally lock guanylate kinase. Delalande O, Sacquin-Mora S, Baaden M. Biophys J 101 1440-1449 (2011)
  16. Purification and characterization of guanylate kinase, a nucleoside monophosphate kinase of Brugia malayi. Gupta S, Yadav S, Singh N, Verma A, Siddiqi I, Saxena JK. Parasitology 141 1341-1352 (2014)
  17. 1H, 13C and 15N resonance assignment of human guanylate kinase. Khan N, Ban D, Trigo-Mourino P, Carneiro MG, Konrad M, Lee D, Sabo TM. Biomol NMR Assign 12 11-14 (2018)


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