List of publications of Stefano Benini


Scientific Papers in international peer reviewed journals:


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

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;

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:/

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)

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)

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)

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)

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

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

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.


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.