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Solution structure of Escherichia coli Par10: The prototypic member of the Parvulin family of peptidyl-prolyl cis/trans isomerases.

Kühlewein A, Voll G, Hernandez Alvarez B, Kessler H, Fischer G, Rahfeld JU, Gemmecker G
Protein Sci 13 2378-87 (2004)
Cited: 21 times
EuropePMC logo PMID: 15322281

Abstract

E. coli Par10 is a peptidyl-prolyl cis/trans isomerase (PPIase) from Escherichia coli catalyzing the isomerization of Xaa-Pro bonds in oligopeptides with a broad substrate specificity. The structure of E. coli Par10 has been determined by multidimensional solution-state NMR spectroscopy based on 1207 conformational constraints (1067 NOE-derived distances, 42 vicinal coupling-constant restraints, 30 hydrogen-bond restraints, and 68 phi/psi restraints derived from the Chemical Shift Index). Simulated-annealing calculations with the program ARIA and subsequent refinement with XPLOR yielded a set of 18 convergent structures with an average backbone RMSD from mean atomic coordinates of 0.50 A within the well-defined secondary structure elements. E. coli Par10 is the smallest known PPIase so far, with a high catalytic efficiency comparable to that of FKBPs and cyclophilins. The secondary structure of E. coli Par10 consists of four helical regions and a four-stranded antiparallel beta-sheet. The N terminus forms a beta-strand, followed by a large stretch comprising three alpha-helices. A loop region containing a short beta-strand separates these helices from a fourth alpha-helix. The C terminus consists of two more beta-strands completing the four-stranded anti-parallel beta-sheet with strand order 2143. Interestingly, the third beta-strand includes a Gly-Pro cis peptide bond. The curved beta-strand forms a hydrophobic binding pocket together with alpha-helix 4, which also contains a number of highly conserved residues. The three-dimensional structure of Par10 closely resembles that of the human proteins hPin1 and hPar14 and the plant protein Pin1At, belonging to the same family of highly homologous proteins.

Articles - 1jns mentioned but not cited (6)

  1. Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA--implications for the catalytic mechanism of parvulins. Heikkinen O, Seppala R, Tossavainen H, Heikkinen S, Koskela H, Permi P, Kilpeläinen I. BMC Struct Biol 9 17 (2009)
  2. Solution structure of Escherichia coli Par10: The prototypic member of the Parvulin family of peptidyl-prolyl cis/trans isomerases. Kühlewein A, Voll G, Hernandez Alvarez B, Kessler H, Fischer G, Rahfeld JU, Gemmecker G. Protein Sci 13 2378-2387 (2004)
  3. Structure and dynamics of the first archaeal parvulin reveal a new functionally important loop in parvulin-type prolyl isomerases. Jaremko Ł, Jaremko M, Elfaki I, Mueller JW, Ejchart A, Bayer P, Zhukov I. J Biol Chem 286 6554-6565 (2011)
  4. Single-domain parvulins constitute a specific marker for recently proposed deep-branching archaeal subgroups. Lederer C, Heider D, van den Boom J, Hoffmann D, Mueller JW, Bayer P. Evol Bioinform Online 7 135-148 (2011)
  5. Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins. Sacquin-Mora S. J R Soc Interface 16 20190075 (2019)
  6. Molecular docking analysis of juglone with parvulin-type PPiase PrsA from Staphylococcus aureus. Dipten L, Amenti, Rajkrishna M. Bioinformation 19 48-52 (2023)


Reviews citing this publication (1)

  1. Prolyl isomerization and its catalysis in protein folding and protein function. Schmidpeter PA, Schmid FX. J Mol Biol 427 1609-1631 (2015)

Articles citing this publication (14)

  1. Penicillin-binding protein folding is dependent on the PrsA peptidyl-prolyl cis-trans isomerase in Bacillus subtilis. Hyyryläinen HL, Marciniak BC, Dahncke K, Pietiäinen M, Courtin P, Vitikainen M, Seppala R, Otto A, Becher D, Chapot-Chartier MP, Kuipers OP, Kontinen VP. Mol Microbiol 77 108-127 (2010)
  2. Dimeric Structure of the Bacterial Extracellular Foldase PrsA. Jakob RP, Koch JR, Burmann BM, Schmidpeter PA, Hunkeler M, Hiller S, Schmid FX, Maier T. J Biol Chem 290 3278-3292 (2015)
  3. The prolyl isomerase domain of PpiD from Escherichia coli shows a parvulin fold but is devoid of catalytic activity. Weininger U, Jakob RP, Kovermann M, Balbach J, Schmid FX. Protein Sci 19 6-18 (2010)
  4. The peptidyl-prolyl isomerase and chaperone Par27 of Bordetella pertussis as the prototype for a new group of parvulins. Hodak H, Wohlkönig A, Smet-Nocca C, Drobecq H, Wieruszeski JM, Sénéchal M, Landrieu I, Locht C, Jamin M, Jacob-Dubuisson F. J Mol Biol 376 414-426 (2008)
  5. Ionic liquids and proteases: a clean alliance for semisynthesis. Wehofsky N, Wespe C, Cerovsky V, Pech A, Hoess E, Rudolph R, Bordusa F. Chembiochem 9 1493-1499 (2008)
  6. Small family with key contacts: par14 and par17 parvulin proteins, relatives of pin1, now emerge in biomedical research. Mueller JW, Bayer P. Perspect Medicin Chem 2 11-20 (2008)
  7. Transient domain interactions enhance the affinity of the mitotic regulator Pin1 toward phosphorylated peptide ligands. Matena A, Sinnen C, van den Boom J, Wilms C, Dybowski JN, Maltaner R, Mueller JW, Link NM, Hoffmann D, Bayer P. Structure 21 1769-1777 (2013)
  8. NMR solution structure and characterization of substrate binding site of the PPIase domain of PrsA protein from Bacillus subtilis. Tossavainen H, Permi P, Purhonen SL, Sarvas M, Kilpeläinen I, Seppala R. FEBS Lett 580 1822-1826 (2006)
  9. Parvulin 17 promotes microtubule assembly by its peptidyl-prolyl cis/trans isomerase activity. Thiele A, Krentzlin K, Erdmann F, Rauh D, Hause G, Zerweck J, Kilka S, Pösel S, Fischer G, Schutkowski M, Schutkowski M, Weiwad M. J Mol Biol 411 896-909 (2011)
  10. Molecular and biochemical characterization of the parvulin-type PPIases in Lotus japonicus. Kouri ED, Labrou NE, Garbis SD, Kalliampakou KI, Stedel C, Dimou M, Udvardi MK, Katinakis P, Flemetakis E. Plant Physiol 150 1160-1173 (2009)
  11. Solution structural analysis of the single-domain parvulin TbPin1. Sun L, Wu X, Peng Y, Goh JY, Liou YC, Lin D, Zhao Y. PLoS One 7 e43017 (2012)
  12. D-amino acid specific proteases and native all-L-proteins: a convenient combination for semisynthesis. Wehofsky N, Pech A, Liebscher S, Schmidt S, Komeda H, Asano Y, Bordusa F. Angew Chem Int Ed Engl 47 5456-5460 (2008)
  13. NmPin from the marine thaumarchaeote Nitrosopumilus maritimus is an active membrane associated prolyl isomerase. Hoppstock L, Trusch F, Lederer C, van West P, Koenneke M, Bayer P. BMC Biol 14 53 (2016)
  14. Identification and functional analysis of a novel parvulin-type peptidyl-prolyl isomerase from Gossypium hirsutum. Wang P, Li XZ, Cui HR, Feng YG, Wang XY. Plant Physiol Biochem 76 58-66 (2014)


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