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Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase.

Schmitzberger F, Kilkenny ML, Lobley CM, Webb ME, Vinkovic M, Matak-Vinkovic D, Witty M, Chirgadze DY, Smith AG, Abell C, Blundell TL
EMBO J 22 6193-204 (2003)
Related entries: 1ppy, 1pqe, 1pqf, 1pqh, 1pt0, 1pt1, 1pyq

Cited: 34 times
EuropePMC logo PMID: 14633979

Abstract

Aspartate decarboxylase, which is translated as a pro-protein, undergoes intramolecular self-cleavage at Gly24-Ser25. We have determined the crystal structures of an unprocessed native precursor, in addition to Ala24 insertion, Ala26 insertion and Gly24-->Ser, His11-->Ala, Ser25-->Ala, Ser25-->Cys and Ser25-->Thr mutants. Comparative analyses of the cleavage site reveal specific conformational constraints that govern self-processing and demonstrate that considerable rearrangement must occur. We suggest that Thr57 Ogamma and a water molecule form an 'oxyanion hole' that likely stabilizes the proposed oxyoxazolidine intermediate. Thr57 and this water molecule are probable catalytic residues able to support acid-base catalysis. The conformational freedom in the loop preceding the cleavage site appears to play a determining role in the reaction. The molecular mechanism of self-processing, presented here, emphasizes the importance of stabilization of the oxyoxazolidine intermediate. Comparison of the structural features shows significant similarity to those in other self-processing systems, and suggests that models of the cleavage site of such enzymes based on Ser-->Ala or Ser-->Thr mutants alone may lead to erroneous interpretations of the mechanism.

Articles - 1pyu mentioned but not cited (1)

  1. Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase. Schmitzberger F, Kilkenny ML, Lobley CM, Webb ME, Vinkovic M, Matak-Vinkovic D, Witty M, Chirgadze DY, Smith AG, Abell C, Blundell TL. EMBO J 22 6193-6204 (2003)


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  2. Structural biology of S-adenosylmethionine decarboxylase. Bale S, Ealick SE. Amino Acids 38 451-460 (2010)
  3. Coenzyme biosynthesis: enzyme mechanism, structure and inhibition. Scott DE, Ciulli A, Abell C. Nat Prod Rep 24 1009-1026 (2007)
  4. How an overlooked gene in coenzyme a synthesis solved an enzyme mechanism predicament. Cronan JE. Mol Microbiol 119 687-694 (2023)

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  2. Biosynthesis of Pantothenic Acid and Coenzyme A. Leonardi R, Jackowski S. EcoSal Plus 2 (2007)
  3. Role of glutamate decarboxylase-like protein 1 (GADL1) in taurine biosynthesis. Liu P, Ge X, Ding H, Jiang H, Christensen BM, Li J. J Biol Chem 287 40898-40906 (2012)
  4. Crystal structure of uncleaved L-aspartate-alpha-decarboxylase from Mycobacterium tuberculosis. Gopalan G, Chopra S, Ranganathan A, Swaminathan K. Proteins 65 796-802 (2006)
  5. 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)
  6. An activator for pyruvoyl-dependent l-aspartate α-decarboxylase is conserved in a small group of the γ-proteobacteria including Escherichia coli. Nozaki S, Webb ME, Niki H. Microbiologyopen 1 298-310 (2012)
  7. Crystallographic snapshot of glycosylasparaginase precursor poised for autoprocessing. Wang Y, Guo HC. J Mol Biol 403 120-130 (2010)
  8. Crystal structure of the schiff base intermediate prior to decarboxylation in the catalytic cycle of aspartate alpha-decarboxylase. Lee BI, Suh SW. J Mol Biol 340 1-7 (2004)
  9. 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)
  10. GADL1 is a multifunctional decarboxylase with tissue-specific roles in β-alanine and carnosine production. Mahootchi E, Cannon Homaei S, Kleppe R, Winge I, Hegvik TA, Megias-Perez R, Totland C, Mogavero F, Baumann A, Glennon JC, Miletic H, Kursula P, Haavik J. Sci Adv 6 eabb3713 (2020)
  11. Structural constraints on autoprocessing of the human nucleoporin Nup98. Sun Y, Guo HC. Protein Sci 17 494-505 (2008)
  12. SEA domain autoproteolysis accelerated by conformational strain: energetic aspects. Sandberg A, Johansson DG, Macao B, Härd T. J Mol Biol 377 1117-1129 (2008)
  13. 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)
  14. Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access. Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. Proteomics 15 2525-2546 (2015)
  15. Structural insights into phosphatidylethanolamine formation in bacterial membrane biogenesis. Cho G, Lee E, Kim J. Sci Rep 11 5785 (2021)
  16. The kirromycin gene cluster of Streptomyces collinus Tü 365 codes for an aspartate-alpha-decarboxylase, KirD, which is involved in the biosynthesis of the precursor beta-alanine. Laiple KJ, Härtner T, Fiedler HP, Wohlleben W, Weber T. J Antibiot (Tokyo) 62 465-468 (2009)
  17. Chemoinformatic identification of novel inhibitors against Mycobacterium tuberculosis L-aspartate α-decarboxylase. Sharma R, Kothapalli R, Van Dongen AM, Swaminathan K. PLoS One 7 e33521 (2012)
  18. The Mechanism of Regulation of Pantothenate Biosynthesis by the PanD-PanZ·AcCoA Complex Reveals an Additional Mode of Action for the Antimetabolite N-Pentyl Pantothenamide (N5-Pan). Arnott ZLP, Nozaki S, Monteiro DCF, Morgan HE, Pearson AR, Niki H, Webb ME. Biochemistry 56 4931-4939 (2017)
  19. Formation of a heterooctameric complex between aspartate α-decarboxylase and its cognate activating factor, PanZ, is CoA-dependent. Monteiro DC, Rugen MD, Shepherd D, Nozaki S, Niki H, Webb ME. Biochem Biophys Res Commun 426 350-355 (2012)
  20. Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins. Jiang Y, Li BQ, Zhang Y, Feng YM, Gao YF, Zhang N, Cai YD. PLoS One 8 e66678 (2013)
  21. Phylogenetic and amino acid conservation analyses of bacterial L-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain. Stuecker TN, Bramhacharya S, Hodge-Hanson KM, Suen G, Escalante-Semerena JC. BMC Res Notes 8 354 (2015)
  22. Significance of Arg3, Arg54, and Tyr58 of L-aspartate α-decarboxylase from Corynebacterium glutamicum in the process of self-cleavage. Cui W, Shi Z, Fang Y, Zhou L, Ding N, Zhou Z. Biotechnol Lett 36 121-126 (2014)
  23. Enhanced poly(3-hydroxypropionate) production via β-alanine pathway in recombinant Escherichia coli. Lacmata ST, Kuiate JR, Ding Y, Xian M, Liu H, Boudjeko T, Feng X, Zhao G. PLoS One 12 e0173150 (2017)
  24. 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)
  25. Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase. Loch JI, Klonecka A, Kądziołka K, Bonarek P, Barciszewski J, Imiolczyk B, Brzezinski K, Gilski M, Jaskolski M. Acta Crystallogr D Struct Biol 78 911-926 (2022)
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  27. Structure of Escherichia coli aspartate α-decarboxylase Asn72Ala: probing the role of Asn72 in pyruvoyl cofactor formation. Webb ME, Lobley CM, Soliman F, Kilkenny ML, Smith AG, Blundell TL, Abell C. Acta Crystallogr Sect F Struct Biol Cryst Commun 68 414-417 (2012)
  28. Discovery and Engineering of a Novel Bacterial L-Aspartate α-Decarboxylase for Efficient Bioconversion. Cui W, Liu H, Ye Y, Han L, Zhou Z. Foods 12 4423 (2023)
  29. Substrate inactivation of bacterial L-aspartate α-decarboxylase from Corynebacterium jeikeium K411 and improvement of molecular stability by saturation mutagenesis. Mo Q, Mao A, Li Y, Shi G. World J Microbiol Biotechnol 35 62 (2019)


Related citations provided by authors (3)

  1. Purification and properties of L-Aspartate-alpha-decarboxylase, an enzyme that catalyzes the formation of beta-alanine in Escherichia coli. Williamson JM, Brown GM J. Biol. Chem. 254 8074-8082 (1979)
  2. Escherichia coli L-aspartate-alpha-decarboxylase: preprotein processing and observation of reaction intermediates by electrospray mass spectrometry. Ramjee MK, Genschel U, Abell C, Smith AG Biochem. J. 323 661-669 (1997)
  3. Crystal structure of aspartate decarboxylase at 2.2A resolution provides evidence for an ester in protein self-processing. Albert A, Dhanaraj V, Genschel U, Khan G, Ramjee MK, Pulido R, Sibanda BL, von Delft F, Witty M, Blundell TL, Smith AG, Abell C Nat. Struct. Biol. 5 289-293 (1998)

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