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Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms.

Tolbert WD, Graham DE, White RH, Ealick SE
Structure 11 285-94 (2003)
Related entries: 1mt1, 1n13

Cited: 18 times
EuropePMC logo PMID: 12623016

Abstract

The three-dimensional structure of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii was determined at 1.4 A resolution. The pyruvoyl group of arginine decarboxylase is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains. The structure of the nonprocessing S53A mutant was also determined. The active site of the processed enzyme unexpectedly contained the reaction product agmatine. The crystal structure confirms that arginine decarboxylase is a homotrimer. The protomer fold is a four-layer alphabetabetaalpha sandwich with topology similar to pyruvoyl-dependent histidine decarboxylase. Highly conserved residues Asn47, Ser52, Ser53, Ile54, and Glu109 are proposed to play roles in the self-processing reaction. Agmatine binding residues include the C terminus of the beta chain (Ser52) from one protomer and the Asp35 side chain and the Gly44 and Val46 carbonyl oxygen atoms from an adjacent protomer. Glu109 is proposed to play a catalytic role in the decarboxylation reaction.

Articles - 1n2m mentioned but not cited (2)

  1. Threonine 57 is required for the post-translational activation of Escherichia coli aspartate α-decarboxylase. Webb ME, Yorke BA, Kershaw T, Lovelock S, Lobley CM, Kilkenny ML, Smith AG, Blundell TL, Pearson AR, Abell C. Acta Crystallogr D Biol Crystallogr 70 1166-1172 (2014)
  2. Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii. Soriano EV, McCloskey DE, Kinsland C, Pegg AE, Ealick SE. Acta Crystallogr D Biol Crystallogr 64 377-382 (2008)


Reviews citing this publication (2)

  1. Polyamines in Eukaryotes, Bacteria, and Archaea. Michael AJ. J Biol Chem 291 14896-14903 (2016)
  2. Structural biology of S-adenosylmethionine decarboxylase. Bale S, Ealick SE. Amino Acids 38 451-460 (2010)

Articles citing this publication (14)

  1. Evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in Bacillus subtilis biofilm formation. Burrell M, Hanfrey CC, Murray EJ, Stanley-Wall NR, Michael AJ. J Biol Chem 285 39224-39238 (2010)
  2. Putrescine biosynthesis in mammalian tissues. Coleman CS, Hu G, Pegg AE. Biochem J 379 849-855 (2004)
  3. Evolutionary links as revealed by the structure of Thermotoga maritima S-adenosylmethionine decarboxylase. Toms AV, Kinsland C, McCloskey DE, Pegg AE, Ealick SE. J Biol Chem 279 33837-33846 (2004)
  4. HdcB, a novel enzyme catalysing maturation of pyruvoyl-dependent histidine decarboxylase. Trip H, Mulder NL, Rattray FP, Lolkema JS. Mol Microbiol 79 861-871 (2011)
  5. The structure of the PanD/PanZ protein complex reveals negative feedback regulation of pantothenate biosynthesis by coenzyme A. Monteiro DCF, Patel V, Bartlett CP, Nozaki S, Grant TD, Gowdy JA, Thompson GS, Kalverda AP, Snell EH, Niki H, Pearson AR, Webb ME. Chem Biol 22 492-503 (2015)
  6. Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains. Giles TN, Fisher DJ, Graham DE. BMC Evol Biol 9 166 (2009)
  7. Synthesis and Deployment of an Elusive Fluorovinyl Cation Equivalent: Access to Quaternary α-(1'-Fluoro)vinyl Amino Acids as Potential PLP Enzyme Inactivators. McCune CD, Beio ML, Sturdivant JM, de la Salud-Bea R, Darnell BM, Berkowitz DB. J Am Chem Soc 139 14077-14089 (2017)
  8. New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments. Cozannet M, Borrel G, Roussel E, Moalic Y, Allioux M, Sanvoisin A, Toffin L, Alain K. Microorganisms 9 E30 (2020)
  9. Reduction of Spermidine Content Resulting from Inactivation of Two Arginine Decarboxylases Increases Biofilm Formation in Synechocystis sp. Strain PCC 6803. Kera K, Nagayama T, Nanatani K, Saeki-Yamoto C, Tominaga A, Souma S, Miura N, Takeda K, Kayamori S, Ando E, Higashi K, Igarashi K, Uozumi N. J Bacteriol 200 e00664-17 (2018)
  10. Identification of mutations restricting autocatalytic activation of bacterial L-aspartate α-decarboxylase. Mo Q, Li Y, Wang J, Shi G. Amino Acids 50 1433-1440 (2018)
  11. Characterization of a Novel Putative S-Adenosylmethionine Decarboxylase-Like Protein from Leishmania donovani. Singh SP, Agnihotri P, Pratap JV. PLoS One 8 e65912 (2013)
  12. Genomic analysis of the polyamine biosynthesis pathway in duckweed Spirodela polyrhiza L.: presence of the arginine decarboxylase pathway, absence of the ornithine decarboxylase pathway, and response to abiotic stresses. Upadhyay RK, Shao J, Mattoo AK. Planta 254 108 (2021)
  13. Preliminary X-ray crystallographic studies of Bacillus subtilis SpeA protein. Liu XY, Lei J, Liu X, Su XD, Li L. Acta Crystallogr Sect F Struct Biol Cryst Commun 65 282-284 (2009)
  14. Structural basis for substrate specificity of l-methionine decarboxylase. Okawa A, Shiba T, Hayashi M, Onoue Y, Murota M, Sato D, Inagaki J, Tamura T, Harada S, Inagaki K. Protein Sci 30 663-677 (2021)


Related citations provided by authors (1)

  1. Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis. Graham DE, Xu H, White RH J. Biol. Chem. 277 23500-23507 (2002)

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