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Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion.

Nakanishi T, Nakatsu T, Matsuoka M, Sakata K, Kato H
Biochemistry 44 1136-44 (2005)
Cited: 14 times
EuropePMC logo PMID: 15667207

Abstract

Pyruvate phosphate dikinase (PPDK) reversibly catalyzes the conversion of ATP, phosphate, and pyruvate into AMP, pyrophosphate, and phosphoenolpyruvate (PEP), respectively. Since the nucleotide binding site (in the N-terminal domain) and the pyruvate/PEP binding site (in the C-terminal domain) are separated by approximately 45 A, it has been proposed that an intermediary domain, called the central domain, swivels between these remote domains to transfer the phosphate. However, no direct structural evidence for the swiveling central domain has been found. In this study, the crystal structures of maize PPDK with and without PEP have been determined at 2.3 A resolution. These structures revealed that the central domain is located near the pyruvate/PEP binding C-terminal domain, in contrast to the PPDK from Clostridium symbiosum, wherein the central domain is located near the nucleotide-binding N-terminal domain. Structural comparisons between the maize and C. symbiosum PPDKs demonstrated that the swiveling motion of the central domain consists of a rotation of at least 92 degrees and a translation of 0.5 A. By comparing the maize PPDK structures with and without PEP, we have elucidated the mode of binding of PEP to the C-terminal domain and the induced conformational changes in the central domain.

Articles - 1vbh mentioned but not cited (3)

  1. Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase. Minges A, Ciupka D, Winkler C, Höppner A, Gohlke H, Groth G. Sci Rep 7 45389 (2017)
  2. On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase. Ciupka D, Gohlke H. Sci Rep 7 8020 (2017)
  3. Investigation into the Mode of Phosphate Activation in the 4-Hydroxy-4-Methyl-2-Oxoglutarate/4-Carboxy-4-Hydroxy-2-Oxoadipate Aldolase from Pseudomonas putida F1. Mazurkewich S, Seah SY. PLoS One 11 e0164556 (2016)


Reviews citing this publication (1)

  1. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Deutscher J, Francke C, Postma PW. Microbiol Mol Biol Rev 70 939-1031 (2006)

Articles citing this publication (10)

  1. Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein. Teplyakov A, Lim K, Zhu PP, Kapadia G, Chen CC, Schwartz J, Howard A, Reddy PT, Peterkofsky A, Herzberg O. Proc Natl Acad Sci U S A 103 16218-16223 (2006)
  2. Posttranslational Modification of Maize Chloroplast Pyruvate Orthophosphate Dikinase Reveals the Precise Regulatory Mechanism of Its Enzymatic Activity. Chen YB, Lu TC, Wang HX, Shen J, Bu TT, Chao Q, Gao ZF, Zhu XG, Wang YF, Wang BC. Plant Physiol 165 534-549 (2014)
  3. Structure of the full-length enzyme I of the phosphoenolpyruvate-dependent sugar phosphotransferase system. Márquez J, Reinelt S, Koch B, Engelmann R, Hengstenberg W, Scheffzek K. J Biol Chem 281 32508-32515 (2006)
  4. Rifampin phosphotransferase is an unusual antibiotic resistance kinase. Stogios PJ, Cox G, Spanogiannopoulos P, Pillon MC, Waglechner N, Skarina T, Koteva K, Guarné A, Savchenko A, Wright GD. Nat Commun 7 11343 (2016)
  5. Prediction of detailed enzyme functions and identification of specificity determining residues by random forests. Nagao C, Nagano N, Mizuguchi K. PLoS One 9 e84623 (2014)
  6. Structural basis of rifampin inactivation by rifampin phosphotransferase. Qi X, Lin W, Ma M, Wang C, He Y, He N, Gao J, Zhou H, Xiao Y, Wang Y, Zhang P. Proc Natl Acad Sci U S A 113 3803-3808 (2016)
  7. Biophysical characterization of the enzyme I of the Streptomyces coelicolor phosphoenolpyruvate:sugar phosphotransferase system. Hurtado-Gómez E, Fernández-Ballester G, Nothaft H, Gómez J, Titgemeyer F, Neira JL. Biophys J 90 4592-4604 (2006)
  8. Small-molecule inhibition of pyruvate phosphate dikinase targeting the nucleotide binding site. Minges A, Groth G. PLoS One 12 e0181139 (2017)
  9. Colorimetric inorganic pyrophosphate assay using a double cycling enzymatic method. Sakasegawa S, Hayashi J, Ikura Y, Ueda S, Imamura S, Kumazawa T, Nishimura A, Ohshima T, Sakuraba H. Anal Biochem 416 61-66 (2011)
  10. Trapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism. Minges A, Höppner A, Groth G. Protein Sci 26 1667-1673 (2017)


Related citations provided by authors (2)

  1. Purification, crystallization and preliminary X-ray diffraction studies on pyruvate phosphate dikinase from maize.. Nakanishi T, Ohki Y, Oda J, Matsuoka M, Sakata K, Kato H Acta Crystallogr D Biol Crystallogr 60 193-4 (2004)
  2. Primary structure of maize pyruvate, orthophosphate dikinase as deduced from cDNA sequence.. Matsuoka M, Ozeki Y, Yamamoto N, Hirano H, Kano-Murakami Y, Tanaka Y J Biol Chem 263 11080-3 (1988)

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