List of publications of Stefano Benini

orcid.org/0000-0001-6299-888X

Scopus: https://www.scopus.com/authid/detail.uri?authorId=7004187955

Scientific Papers in international peer reviewed journals:

Poonsiri T, Stransky J, Demitri N, Haas H, Cianci M, Benini S. SidF, a dual substrate N5-acetyl-N5-hydroxy-L-ornithine transacetylase involved in Aspergillus fumigatus siderophore biosynthesis. Journal of Structural Biology: X 11 (2025) 100119  https://doi.org/10.1016/j.yjsbx.2024.100119

Poonsiri, T.; Dell’Accantera, D.; Loconte, V.; Casnati, A.; Cervoni, L.; Arcovito, A.; Benini, S.; Ferrari, A.; Cipolloni, M.; Cacioni, E.; et al. 3-O-Methyltolcapone and Its Lipophilic Analogues Are Potent Inhibitors of Transthyretin Amyloidogenesis with High Permeability and Low Toxicity. Int. J. Mol. Sci. (2024), 25, 479. https://doi.org/10.3390/ijms250104792.      

Albani, S.; Polsinelli, I.; Mazzei, L.; Musiani, F.; Benini, S. Determination and Kinetic Characterization of a New Potential Inhibitor for AmsI Protein Tyrosine Phosphatase from the Apple Pathogen Erwinia amylovora. Molecules 2023, 28, 7774. https:// doi.org/10.3390/molecules28237774

Carlini L.; Esposito, A.; Ambrosino, L.; Bharti, S.; Invernizzi, L., M.; Piazza, S.; Benini, S. The ams proteins and the amylovoran biosynthetic pathway: an extensive bioinformatic studyJournal of Plant Pathology 2023-11-08 | Journal article DOI: 1007/s42161-023-01532-9

Polsinelli I, Salomone-Stagni M, Benini S (2022). Erwinia tasmaniensis levansucrase shows enantiomer selection for (S)-1,2,4-butanetriol . ACTA CRYSTALLOGRAPHICA. SECTION F, STRUCTURAL BIOLOGY COMMUNICATIONS, vol. 78, p. 289-296, ISSN: 2053-230X, doi: 10.1107/S2053230X2200680X

Carlini, L.; Tancreda, G.; Iobbi, V.; Caicci, F.; Bruno, S.; Esposito, A.; Calzia, D.; Benini, S.; Bisio, A.; Manni, L.; Schito, A., Traverso, C. E., Ravera, S..  and Panfoli I. The Flavone Cirsiliol from Salvia x jamensis Binds the F1 Moiety of ATP Synthase, Modulating Free Radical Production. Cells 2022, 11, 3169. https://doi.org

Caliandro, R., Polsinelli, I., Demitri, N., Musiani, F., Martens, S., Benini, S. The structural and functional characterization of Malus domestica double bond reductase MdDBR provides insights towards the identification of its substrates (2021) International Journal of Biological Macromolecules, 171, pp. 89-99 DOI: 10.1016/j.ijbiomac.2020.12.190

Benini, S. Structural and functional characterization of proteins from the fire blight pathogen Erwinia amylovora. A review on the state of the art (2020) Journal of Plant Pathology, DOI: 10.1007/s42161-020-00682-4

Benini, S. Carbohydrate-active enzymes: Structure, activity, and reaction products. Int. J. Mol. Sci.  (2020), 21 (8), 2727 https://doi.org/10.3390/ijms21082727

Polsinelli, I., Caliandro, R., Demitri, N., Benini, S. The Structure of Sucrose-Soaked Levansucrase Crystals from Erwinia tasmaniensis reveals a Binding Pocket for Levanbiose. Int. J. Mol. Sci. (2020), 21(1), 83; https://doi.org/10.3390/ijms21010083

Mazzei, L., Cianci, M., Benini, S., Ciurli, S. The impact of pH on catalytically critical protein conformational changes: the case of the urease, a nickel enzyme. Chemistry (2019) https:/doi.org/10.1002/chem.201902320

Bartho, J.D., Demitri, N., Bellini, D., Flachowsky, H., Peil, A., Walsh, M.A., Benini, S. The structure of Erwinia amylovora AvrRpt2 provides insight into protein maturation and induced resistance to fire blight by Malus x robusta 5. J. Struct. Biol. (2019) https://doi.org/10.1016/j.jsb.2019.03.010

Benini, S., Haouz, A., Proux, F., Alzari, P., Wilson, K. The crystal structure of Rv2991 from Mycobacterium tuberculosis: An F420 binding protein with unknown function. J. Struct. Biol. (2019) https://doi.org/10.1016/j.jsb.2019.03.006

Mazzei, L., Cianci, M., Benini, S., Ciurli, S.. The structure of the elusive urease-urea complex unveils a paradigmatic case of metallo-enzyme catalysis. Angew. Chem. Int. Ed Engl. (2019) https://doi.org/10.1002/anie.201903565

Polsinelli, I., Borruso, L., Caliandro, R., Triboli, L., Esposito, A., and Benini, S. (2019) A genome-wide analysis of desferrioxamine mediated iron uptake in Erwinia spp. reveals genes exclusive of the rosaceae infecting strains. Scientific Reports. 9, 2818. DOI:10.1038/s41598-019-39787-x

Polsinelli, I., Caliandro, R., Salomone-Stagni, M., Demitri, N., Rejzek, M., Field, R.A., Benini, S., 2019. Comparison of the Levansucrase from the epiphyte Erwinia tasmaniensis vs its homologue from the phytopathogen Erwinia amylovora. Int. J. Biol. Macromol. 127, pp. 496-501. DOI:10.1016/j.ijbiomac.2019.01.074

Salomone-Stagni, M., Bartho, J.D., Kalita, E., Rejzek, M., Field, R.A., Bellini, D., Walsh, M.A., Benini, S. Structural and functional analysis of Erwinia amylovora SrlD. The first crystal structure of a sorbitol-6-phosphate 2-dehydrogenase J. Struc. Biol. (2018), 203, pp 109-119 DOI:10.1016/j.jsb.2018.03.010

Salomone-Stagni M., Bartho, J. D., Polsinelli I., Bellini D., Walsh M. A., Demitri N., Benini S. A complete structural characterization of the desferrioxamine E biosynthetic pathway from the fire blight pathogen Erwinia amylovora, J. Struc. Biol. (2018) doi.org/10.1016/j.jsb.2018.02.002

Benini⁠⁠ S., Toccafondi⁠ M., Rejzek M., Musiani F., Wagstaff⁠ B., A., Wuerges J., Cianci⁠ M., Field R., A. Glucose-1-phosphate uridylyltransferase from Erwinia amylovora: Activity, structure and substrate specificity, BBA – Proteins and Proteomics (2017) 1865 pp 1348-1357 DOI 10.1016/j.bbapap.2017.08.015

Borruso L., Salomone-Stagni M., Polsinelli I, Schmitt A.,O., Benini S. Conservation of Erwinia amylovora pathogenicity-relevant genes among Erwinia genomes. (2017) Archives of microbiology DOI 10.1007/s00203-017-1409-7

Bartho, J. D., Bellini D., Wuerges J., Demitri N., Toccafondi M, Schmitt A. O., Zhao Y, Walsh M A., Benini S. The crystal structure of Erwinia amylovora AmyR, a member of the YbjN protein family, shows similarity to type III secretion chaperones but suggests different cellular functions. PLoS ONE (2017) 12(4): e0176049 https://doi.org/10.1371/journal.pone.0176049

Salomone-Stagni, M., Musiani, F. and Benini, S.  Characterization and 1.57 Å resolution structure of the key fire blight phosphatase AmsI from Erwinia amylovora Acta Cryst. (2016). F 72, 903-910 https://doi.org/10.1107/S2053230X16018781

Mazzei, L.; Cianci, M.; Benini, S.; Bertini, L.; Musiani, F.; Ciurli, S. Kinetic and structural studies reveal a unique binding mode of sulfite to the nickel center in urease. Journal of Inorganic Biochemistry (2015 online version) 2016 (printed version), 154, 42–49 DOI    10.1016/J.JINORGBIO.2015.11.003

Wuerges, J., Caputi, L., Cianci, M., Boivin, S., Meijers, R., Benini, S. The crystal structure of Erwinia amylovora levansucrase provides a snapshot of the products of sucrose hydrolysis trapped into the active site Journal of Structural Biology 191 (2015), pp. 290-298 DOI: 10.1016/j.jsb.2015.07.010

Wagstaff,^, A.,^, Rejzek M., Tedaldi, L.M., Caputi L., O’Neill E.C., Benini S., Wagner G. K., Field R. A. Enzymatic synthesis of nucleobase-modified UDP-sugars: scope and limitations. Carbohydrate Res. Volume 404, 17-25 (2015). doi:10.1016/j.carres.2014.12.005

Benini, S., Caputi, L., and Cianci, M. Cloning, purification, crystallization and 1.57 angstrom resolution X-ray data analysis of AmsI, the tyrosine phosphatase controlling amylovoran biosynthesis in the plant pathogen Erwinia amylovora. Acta Crystallographica Section F-Structural Biology Communications. 70, 1693-1696 (2014) doi:10.1107/S2053230X14024947

Toccafondi M., Cianci M., Benini S. Expression, purification, crystallization and preliminary X-ray analysis of glucose-1-phosphate uridylyltransferase (GalU) from Erwinia amylovora Acta Crystallographica Section F: Structural Biology Communications, Volume 70, Part 9, pages 1249-1251 (2014). doi:10.1107/S2053230X14016458

Benini S., Cianci M., Mazzei L., Ciurli S. Fluoride inhibition of Sporosarcina pasteurii urease: structure and thermodynamics. J. Biol. Inorg. Chem., Volume 19, Issue 8, Page 1243-1261 (2014). DOI 10.1007/s00775-014-1182-x

Caputi L., Nepogodiev S. A., Malnoy M., Rejzek M., Field R.A., Benini S., Biomolecular Characterization of the Levansucrase of Erwinia amylovora, a Promising Biocatalyst for the Synthesis of Fructooligosaccharides J. Agric. Food Chem., vol. 61, 12265−12273, (2013) doi:10.1021/jf4023178

L. Caputi, M. Cianci, S. Benini.  Cloning, expression, purification, crystallization and preliminary X-ray analysis of EaLsc, a levansucrase from Erwinia amylovora. Acta Cryst. (2013),  F69, 570-573 doi:10.1107/S1744309113010750

S. Benini, M. Chechik, M. Ortiz Lombardìa, S. Polier, A. Leech, M. B. Shevtsov, and J. C. Alonso. The 1.58 Å resolution structure of the DNA-binding domain of bacteriophage SF6 small terminase provides new hints on DNA binding. Acta Cryst. (2013),  F69, 376-381. doi:10.1107/S1744309113004399

S. Benini,  P. Kosikowska, M. Cianci, L. Mazzei,  A. Gonzalez Vara,  Ł. Berlicki, and S. Ciurli. The crystal structure of Sporosarcina pasteurii urease in a complex with citrate provides new hints for inhibitor design. J. Biol. Inorg. Chem. (2013), 18, 391-399. DOI 10.1007/s00775-013-0983-7

C. R. Büttner, M. Chechik, M. Ortiz-Lombardía, C. Smits, I. Ebong, V. Chechik, G. Jeschke, E. Dykeman, S. Benini, C. V. Robinson, J. C. Alonso, and A. A. Antson.  Structural basis for DNA recognition and loading into a viral packaging motor. PNAS., (2012), 109, 811-816 DOI: 10.1073/pnas.1110270109

B. Zambelli, F. Musiani, S. Benini, and S.Ciurli. Chemistry of Ni⁽²⁺⁾ in urease: sensing, trafficking, and catalysis. Accounts of chemical research (2011), 44, 520-530 DOI: 10.1021/ar200041k

S. Benini, M. Cianci, and S. Ciurli.  Holo-Ni2+ Helicobacter pylori NikR contains four square-planar nickel-binding sites at physiological pH. Dalton Trans., (2011), 40, 7831-7833 DOI: 10.1039/c1dt11107h

S. Benini, and K. S. Wilson. Structure of the Mycobacterium tuberculosis soluble inorganic pyrophosphatase Rv3628 at pH 7.0. Acta Cryst. (2011). F67, 866–870 doi:10.1107/S1744309111023323

S. Benini, W. R. Rypniewski, K. S. Wilson, and S. Ciurli. High Resolution Crystal Structure of Rubrivivax gelatinosus cytochrome c’. J. Inorg. Bioch. (2008), 102, 1322-1328.

M. Tammenkoski, S. Benini, N. N. Magretova, A. A. Baykov, and R. Lahti. An Unusual, His-dependent Family I Pyrophosphatase from Mycobacterium tuberculosis. J. Biol. Chem. (2005), 280, 41819-41826.

S. Benini, W. R. Rypniewski, K. S. Wilson, S. Mangani and S. Ciurli. Molecular Details of Urease Inhibition by Borate: Insights into the catalytic Mechanism. J. Am. Chem Soc. (2004), 126, 3714-3715.

A. González, S. Benini, and S. Ciurli. Crystal Structure of Rhodoferax fermentans High Potential Iron-sulfur Protein Solved by MAD. Acta Cryst. (2003), D59, 1582-1588.

S. Benini, W. R. Rypniewski, K. S. Wilson, S. Ciurli and S. Mangani. Structure-Based Rationalization of Urease Inhibition by Phosphate: Novel Insights into the Enzyme Mechanism. J. Biol. Inorg. Chem. (2001), 6, 778-790. DOI: 10.1007/s007750100254

S. Benini, A. González, W.R. Rypniewski, K.S. Wilson, J.J. Van Beeumen, S. Ciurli. Crystal Structure of Oxidized Bacillus pasteurii Cytochrome c₅₅₃ at 0.97-Å Resolution. Biochemistry. (2000), 39, 13115-13126. DOI: 10.1021/bi000402j

S. Benini, W.R. Rypniewski, K.S. Wilson, S. Miletti, S. Ciurli, S. Mangani. The Complex of Bacillus pasteurii Urease with Acetohydroxamate Anion from X-Ray Data at 1.55 Å Resolution. J. Biol. Inorg. Chem. (2000), 5, 110-118. DOI: 10.1007/s007750050014

I.H.M. Vandenberghe, Y. Guisez, S. Ciurli, S. Benini, J.J. Van Beeumen. Cytochrome c-553 from the Alkalophilic Bacterium Bacillus pasteurii has the Primary Structure Characteristics of a Lipoprotein. Biochem. Biophys. Res. Commun. (1999), 264, 380-387.

A. González, J-D. Pédelacq, M. Solà, F.X. Gomis-Rüth, M. Coll, J-P.Samama, S. Benini. Two-Wavelength MAD Phasing: in Search of the Optimal Choice of Wavelengths. Acta Cryst. (1999), D55, 1449-1458.

S. Ciurli, S. Benini, W. R. Rypniewski, K. S. Wilson, S. Miletti, S. Mangani. Structural Properties of the Nickel Ions in Urease: Novel Insights into the Catalytic and Inhibition Mechanism. Coord. Chem. Rev. (1999), 190, 331-355.

S. Benini, W. R. Rypniewski, K. S. Wilson, S. Miletti, S. Ciurli , S. Mangani. A New Proposal for Urease Mechanism Based on the Crystal Structures of the Native and the Inhibited Enzyme from Bacillus pasteurii: Why Urea Hydrolysis Costs Two Nickels. Structure, (1999), 7, 205-216.        doi:10.1016/S0969-2126(99)80026-4

S. Benini, M. Borsari, S. Ciurli, A. Dikiy, M. Lamborghini. Modulation of Bacillus pasteurii Cytochrome c₅₅₃ Reduction Potential by Structural and Solution Parameters. J. Bio. Inorg. Chem., (1998), 3, 371-382. DOI: 10.1007/s007750050247

S. Benini, S. Ciurli, W. R. Rypniewski, K. S. Wilson, S. Mangani. The Complex of Bacillus pasteurii Urease with β-Mercaptoethanol from X-ray Data at 1.65 Å Resolution. J. Bio. Inorg. Chem., (1998), 3, 268-273. DOI: 10.1007/s007750050231

S. Benini, S. Ciurli, W. R. Rypniewski, K. S. Wilson, S. Mangani. Crystallization and Preliminary High-Resolution X-Ray Diffraction Analysis of Native and β-Mercaptoethanol-Inhibited Urease from Bacillus pasteurii. Acta Cryst., (1998), D54, 409-412.

S. Benini, W. R. Rypniewski, K. S. Wilson, S. Ciurli. Crystallization and Preliminary X-ray Diffraction Analysis of Cytochrome c‘ from Rubrivivax gelatinosus at 1.3 Å Resolution. Acta Cryst. (1998), D54, 284-287.

S. Benini, S. Ciurli, W. R. Rypniewski, K. S. Wilson. Crystals of Cytochrome c-553 from Bacillus pasteurii Show Diffraction to 0.97 Å Resolution. Proteins: Struc., Func., Genet., (1997), 28, 580-585.

M. Borsari, S. Benini, D. Marchesi, S. Ciurli. Cyclic Voltammetry and Spectroelectrochemistry of Cytochrome c8 from Rubrivivax gelatinosus. Implications in Photosynthetic Electron Transfer. Inorg. Chim. Acta (1997), 263, 379-384.

S. Benini, S. Ciurli, S. Mangani, H. F. Nolting. X-ray Absorption Spectroscopy Study of Native and Phenylphosphorodiamidate-Inhibited Bacillus pasteurii Urease. Eur. J . Biochem., (1996), 239, 61-66.

S. Ciurli, C. Marzadori, S. Benini, S. Deiana, C. Gessa. Urease from the Soil Bacterium Bacillus pasteurii. Immobilization on Ca-polygalacturonate. Soil Biol. Biochem., (1996), 28, 811-817.

S. Benini, C. Gessa, S. Ciurli. Bacillus pasteurii Urease: a Heteropolimeric Enzyme with a Binuclear Nickel Active Site. Soil Biol. Biochem., (1996), 28, 819-821.

S. Benini, S. Ciurli, C. Luchinat. Oxidized and reduced [Fe₂Q₂] (Q=S,Se) Cores of Spinach Ferredoxin: a Comparative Study Using ¹H NMR Spectroscopy. Inorg. Chem., (1995), 34, 417-420.

Books:

S. Benini, (2010), Structure and function of urease and cytochrome c-553. Saarbruecken, DE: ed. LAP Lambert Academic Publishing, ISBN: 978-3-8383-6498-8

Contribution to books:

Benini S, Musiani F and Ciurli S (2013). Urease. In:  Kretsinger RH, Uversky VN, Permyakov EA (eds). Encyclopedia of Metalloproteins. Springer, New York, pp. 2287-2292 ISBN: 978-1-4614-1532-9 (Print) 978-1-4614-1533-6 (Online)

M. Cremonini, O. Francioso, S. Benini, S. Ciurli. Quantification of Bacillus pasteurii Urease Secondary Structure by Factor Analysis of FT-IR Spectra. P. Carmona et al. (eds.) Spectroscopy of Biological Molecules: Modern trends, 173-174. 1997 Kluwer Academic Publisher. Printed in the Netherlands. DOI: 10.1007/978-94-011-5622-6_77

Conference Proceedings:

S. Benini, J.D. Bartho, M. Salomone-Stagni, M. Toccafondi. Investigating the molecular basis of fire blight by structural and functional genomics of Erwinia amylovora Proceedings of the Thirteen International Workshop on Fire Blight,02-05/07/2013. Eds.: F. Rezzonico, T.H.M. Smits and E. Holliger, Acta Hort. 1056:161-164, ISHS 2014. DOI:10.17660/ActaHortic.2014.1056.24

Papers in italian journals:

A. Bratti, S. Benini. Allevamento «in vitro» delle larve di Pseudogonia rufifrons Wied. (Dipt. Tachinidae). Prove su diete subnaturali e meridiche. Boll. Ist. Ent. “G. Grandi” (1992), 46, 71-85.