The full-length Streptococcus pneumoniae major pilin RrgB crystallizes in a fibre-like structure, which presents the D1 isopeptide bond and provides details on the mechanism of pilus polymerization

2012 ◽  
Vol 441 (3) ◽  
pp. 833-843 ◽  
Author(s):  
Lamya El Mortaji ◽  
Carlos Contreras-Martel ◽  
Monica Moschioni ◽  
Ilaria Ferlenghi ◽  
Clothilde Manzano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Streptococcus Pneumoniae ◽  
Crystal Packing ◽  
Full Length ◽  
Intermolecular Bond ◽  
Isopeptide Bond ◽  
Live Bacteria ◽  
Sorting Motif ◽  
Density Map ◽  
First Time

RrgB is the major pilin which forms the pneumococcal pilus backbone. We report the high-resolution crystal structure of the full-length form of RrgB containing the IPQTG sorting motif. The RrgB fold is organized into four distinct domains, D1–D4, each of which is stabilized by an isopeptide bond. Crystal packing revealed a head-to-tail organization involving the interaction of the IPQTG motif into the D1 domain of two successive RrgB monomers. This fibrillar assembly, which fits into the electron microscopy density map of the native pilus, probably induces the formation of the D1 isopeptide bond as observed for the first time in the present study, since neither in published structures nor in soluble RrgB produced in Escherichia coli or in Streptococcus pneumoniae is the D1 bond present. Experiments performed in live bacteria confirmed that the intermolecular bond linking the RrgB subunits takes place between the IPQTG motif of one RrgB subunit and the Lys183 pilin motif residue of an adjacent RrgB subunit. In addition, we present data indicating that the D1 isopeptide bond is involved in RrgB stabilization. In conclusion, the crystal RrgB fibre is a compelling model for deciphering the molecular details required to generate the pneumococcal pilus.

scholarly journals Structural and Biochemical Studies of Dihydrofolate Reductase from Streptococcus pyogenes as a Target for Antifolate Antibiotics

2018 ◽  
Author(s):  
Behnoush Hajian ◽  
Jolanta Krucinska ◽  
Michael Martins ◽  
Narendran G-Dayanan ◽  
Kishore Viswanathan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Streptococcus Pyogenes ◽  
Dihydrofolate Reductase ◽  
Wide Spectrum ◽  
Streptococcal Infections ◽  
Biochemical Studies ◽  
Live Bacteria ◽  
Dhfr Inhibitors ◽  
First Time ◽  
Structural Insights

ABSTRACTStreptococcus pyogenes, a beta-hemolytic bacterium, causes a wide spectrum of infections in human including pharyngitis, tonsillitis, scarlet fever, rheumatic fever, and necrotizing fasciitis. Streptococcal infections can also exist as co-infection with methicillin resistant Staphylococcus aureus (MRSA). Trimethoprim-sulfamethoxazole (TMP-SMX) combination has been used for treatment of S. pyogenes and MRSA co-infection. However, resistance to TMP, an inhibitor of dihydrofolate reductase enzyme (DHFR), has challenged the efficacy of TMP-SMX combination. We explored the activity of a series of novel DHFR inhibitors against S. pyogenes. This study identified potent inhibitors of DHFR enzyme from S. pyogenes with excellent inhibitory activity against the growth of the live bacteria. We determined, for the first time, the crystal structure of S. pyogenes DHFR which provides structural insights into design and development of antifolate agents against this global pathogen.

scholarly journals Crystal Structure of Mouse Thymidylate Synthase in Tertiary Complex with dUMP and Raltitrexed Reveals N-Terminus Architecture and Two Different Active Site Conformations

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Anna Dowierciał ◽  
Piotr Wilk ◽  
Wojciech Rypniewski ◽  
Wojciech Rode ◽  
Adam Jarmuła
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Thymidylate Synthase ◽  
Active Site ◽  
Crystal Packing ◽  
Terminal Segment ◽  
Asymmetrical Effect ◽  
Active Site Cleft ◽  
Ligand Free ◽  
First Time

The crystal structure of mouse thymidylate synthase (mTS) in complex with substrate dUMP and antifolate inhibitor Raltitrexed is reported. The structure reveals, for the first time in the group of mammalian TS structures, a well-ordered segment of 13 N-terminal amino acids, whose ordered conformation is stabilized due to specific crystal packing. The structure consists of two homodimers, differing in conformation, one being more closed (dimer AB) and thus supporting tighter binding of ligands, and the other being more open (dimer CD) and thus allowing weaker binding of ligands. This difference indicates an asymmetrical effect of the binding of Raltitrexed to two independent mTS molecules. Conformational changes leading to a ligand-induced closing of the active site cleft are observed by comparing the crystal structures of mTS in three different states along the catalytic pathway: ligand-free, dUMP-bound, and dUMP- and Raltitrexed-bound. Possible interaction routes between hydrophobic residues of the mTS protein N-terminal segment and the active site are also discussed.

Crystal Packing of Odd-Chain Saturated Triglycerides

1983 ◽  
Vol 38 (7-8) ◽  
pp. 511-514 ◽  
Author(s):  
Douglas L. Dorset
Keyword(s):  
Crystal Structure ◽  
Melting Point ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Crystal Packing ◽  
Electron Diffraction Data ◽  
Chain Packing ◽  
Crystal Electron ◽  
First Time ◽  
End Group

Single crystal electron diffraction data from an odd-chain triglyceride, glycerol triheptadecanoate, are compared with the known structure of the even-chain homo-acid triglycerides. Both class­es of triglycerides are found to resemble one another in chain packing: they both have the same chain tilt (61 °) for the β-polymorph and, further, the orientation of the T∥ subcell in the crystal structure is identical. The existence of the T∥ subcell is quantitatively verified for the first time with the diffraction intensities from suitably tilted crystals. Given these similarities in β-poly­morph structure, the major difference between triglycerides with even or odd chains (indicated by published long spacing and melting point alternation) must be due to the methyl end group pack­ing - i.e., the end group packing volume for the odd-chain glycerides must be larger than found for the even-chain materials.

scholarly journals A new crystal form of Lys48-linked diubiquitin

2010 ◽  
Vol 66 (9) ◽  
pp. 994-998 ◽  
Author(s):  
Jean-François Trempe ◽  
Nicholas R. Brown ◽  
Martin E. M. Noble ◽  
Jane A. Endicott
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Crystal Form ◽  
Asymmetric Unit ◽  
Polyubiquitin Chains ◽  
Isopeptide Bond ◽  
Closed Conformation ◽  
Crystallization Conditions

Lys48-linked polyubiquitin chains are recognized by the proteasome as a tag for the degradation of the attached substrates. Here, a new crystal form of Lys48-linked diubiquitin (Ub2) was obtained and the crystal structure was refined to 1.6 Å resolution. The structure reveals an ordered isopeptide bond in atransconfiguration. All three molecules in the asymmetric unit were in the same closed conformation, in which the hydrophobic patches of both the distal and the proximal moieties interact with each other. Despite the different crystallization conditions and different crystal packing, the new crystal structure of Ub2is similar to the previously published structure of diubiquitin, but differences are observed in the conformation of the flexible isopeptide linkage.

scholarly journals Investigation of Solubility Behavior of Canagliflozin Hydrate Crystals Combining Crystallographic and Hirshfeld Surface Calculations

Molecules ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 298
Author(s):  
Yefen Zhu ◽  
Yanlei Kang ◽  
Ling Zhu ◽  
Kaxi Yu ◽  
Shuai Chen ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Intermolecular Forces ◽  
Hirshfeld Surface ◽  
Reversible Inhibitor ◽  
Solubility Behavior ◽  
Hydrogen Bond Networks ◽  
Solvent Molecules ◽  
First Time ◽  
Better Than

Canagliflozin (CG) was a highly effective, selective and reversible inhibitor of sodium-dependent glucose co-transporter 2 developed for the treatment of type 2 diabetes mellitus. The crystal structure of CG monohydrate (CG-H2O) was reported for the first time while CG hemihydrate (CG-Hemi) had been reported in our previous research. Solubility and dissolution rate results showed that the solubility of CG-Hemi was 1.4 times higher than that of CG-H2O in water and hydrochloric acid solution, and the dissolution rates of CG-Hemi were more than 3 folds than CG-H2O in both solutions. Hirshfeld surface analysis showed that CG-H2O had stronger intermolecular forces than CG-Hemi, and water molecules in CG-H2O participated three hydrogen bonds, forming hydrogen bond networks. These crystal structure features might make it more difficult for solvent molecules to dissolve CG-H2O than CG-Hemi. All these analyses might explain why the dissolution performance of CG-Hemi was better than CG-H2O. This work provided an approach to predict the dissolution performance of the drug based on its crystal structure.

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