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Crystallographic proof for an extended hydrogen-bonding network in small prolyl isomerases.

Mueller JW, Link NM, Matena A, Hoppstock L, Rüppel A, Bayer P, Blankenfeldt W
J Am Chem Soc 133 20096-9 (2011)
Cited: 22 times
EuropePMC logo PMID: 22081960

Abstract

Parvulins compose a family of small peptidyl-prolyl isomerases (PPIases) involved in protein folding and protein quality control. A number of amino acids in the catalytic cavity are highly conserved, but their precise role within the catalytic mechanism is unknown. The 0.8 Å crystal structure of the prolyl isomerase domain of parvulin Par14 shows the electron density of hydrogen atoms between the D74, H42, H123, and T118 side chains. This threonine residue has previously not been associated with catalysis, but a corresponding T152A mutant of Pin1 shows a dramatic reduction of catalytic activity without compromising protein stability. The observed catalytic tetrad is strikingly conserved in Pin1- and parvulin-type proteins and hence constitutes a common feature of small peptidyl prolyl isomerases.

Reviews - 3ui4 mentioned but not cited (2)

  1. Macromolecular ab initio phasing enforcing secondary and tertiary structure. Millán C, Sammito M, Usón I. IUCrJ 2 95-105 (2015)
  2. Roles of Prolyl Isomerases in RNA-Mediated Gene Expression. Thapar R. Biomolecules 5 974-999 (2015)

Articles - 3ui4 mentioned but not cited (7)

  1. 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)
  2. 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)
  3. How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity. Carugo O. Amino Acids 53 779-782 (2021)
  4. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)
  5. An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. Rosenberg AA, Yehishalom N, Marx A, Bronstein AM. Proc Natl Acad Sci U S A 120 e2301064120 (2023)
  6. Structural Analysis of the 42 kDa Parvulin of Trypanosoma brucei. Rehic E, Hoenig D, Kamba BE, Goehring A, Hofmann E, Gasper R, Matena A, Bayer P. Biomolecules 9 E93 (2019)
  7. The oxygen-oxygen distance of water in crystallographic data sets. Palese LL. Data Brief 28 105076 (2020)


Reviews citing this publication (1)

  1. Structure and function of the human parvulins Pin1 and Par14/17. Matena A, Rehic E, Hönig D, Kamba B, Bayer P. Biol Chem 399 101-125 (2018)

Articles citing this publication (12)

  1. Pin1 inhibitors: Pitfalls, progress and cellular pharmacology. Moore JD, Potter A. Bioorg Med Chem Lett 23 4283-4291 (2013)
  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. Dynamic Allostery Modulates Catalytic Activity by Modifying the Hydrogen Bonding Network in the Catalytic Site of Human Pin1. Wang J, Kawasaki R, Uewaki JI, Rashid AUR, Tochio N, Tate SI. Molecules 22 E992 (2017)
  4. Parvulin 17-catalyzed Tubulin Polymerization Is Regulated by Calmodulin in a Calcium-dependent Manner. Burgardt NI, Schmidt A, Manns A, Schutkowski A, Jahreis G, Lin YJ, Schulze B, Masch A, Lücke C, Weiwad M. J Biol Chem 290 16708-16722 (2015)
  5. Characterisation of SEQ0694 (PrsA/PrtM) of Streptococcus equi as a functional peptidyl-prolyl isomerase affecting multiple secreted protein substrates. Ikolo F, Zhang M, Harrington DJ, Robinson C, Waller AS, Sutcliffe IC, Black GW. Mol Biosyst 11 3279-3286 (2015)
  6. Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases. Czajlik A, Kovács B, Permi P, Gáspári Z. Sci Rep 7 44504 (2017)
  7. Against the odds? De novo structure determination of a pilin with two cysteine residues by sulfur SAD. Gorgel M, Bøggild A, Ulstrup JJ, Weiss MS, Müller U, Nissen P, Boesen T. Acta Crystallogr D Biol Crystallogr 71 1095-1101 (2015)
  8. Design and Synthesis of Oligopeptidic Parvulin Inhibitors. Relitti N, Prasanth Saraswati A, Carullo G, Papa A, Monti A, Benedetti R, Passaro E, Brogi S, Calderone V, Butini S, Gemma S, Altucci L, Campiani G, Doti N. ChemMedChem 17 e202200050 (2022)
  9. ¹H, ¹³C and ¹⁵N resonance assignments of human parvulin 17. Lin YJ, Schmidt A, Burgardt NI, Thiele A, Weiwad M, Lücke C. Biomol NMR Assign 7 325-329 (2013)
  10. Mechanistic insights into Pin1 peptidyl-prolyl cis-trans isomerization from umbrella sampling simulations. Di Martino GP, Masetti M, Cavalli A, Recanatini M. Proteins 82 2943-2956 (2014)
  11. A Redox-Sensitive Cysteine Is Required for PIN1At Function. Selles B, Dhalleine T, Boutilliat A, Rouhier N, Couturier J. Front Plant Sci 12 735423 (2021)
  12. Expression, Purification, Structural and Functional Characterization of Recombinant Human Parvulin 17. Monti A, Ronca R, Campiani G, Ruvo M, Doti N. Mol Biotechnol 65 337-349 (2023)


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