Extended conformation of putrescine occurring on a center of symmetry in its 1:2 complex with malonic acid

The 1,4-butane diammonium (putrescine) crystalizes with propanedioic acid (malonic monoanions in space group Pcab (1,4-butane diammonium hydrogen propanedioate, C4H14N22+.2C(3)H(3)O(4)(-)). One of the carboxylate moieties of malonic acid is protonated. The asymmetric unit of the crystal contains one molecule of malonic acid and half a molecule of putrescine. All three H atoms of the putrescine amino groups participate in hydrogen bonding

Molecular dynamics studies on the domain swapped <i>Salmonella typhimurium</i> survival protein SurE: insights on the possible reasons for catalytic cooperativity

<p>Stationary phase survival protein SurE from <i>Salmonella typhimurium</i> is a dimeric protein formed by the swapping of a tetramerization loop involved in the formation of a loose tetramer and a C-terminal helix. It functions as a phosphatase. The two-fold symmetry of the dimeric protein was lost in the mutants H234A and D230A/H234A in which a crucial hydrogen bond in the hinge involved in C-terminal helix swapping was eliminated. The catalytic activity of both mutants was drastically reduced. In contrast to the native protein, H234A exhibited positive cooperativity in its catalytic activity. In order to relate these observations to the dynamics of the native and distorted mutants, molecular dynamics (MD) simulations were carried out using GROMACS v4.0.7. In all the simulations, the swapped segments and a segment near the active site were found to be highly flexible. These segments exhibited distinct dynamic features in the two protomers (A and B) of the dimeric protein. The dimeric organization was more significantly affected in the mutants when compared to the native structure, suggesting that the mutations enhance the intrinsic flexibility of the protein. The larger flexibility of the mutants affects the relative movement between the loops near the two active sites. The positive cooperativity observed in H234A mutant is most likely due to this increased flexibility and loop movement.</p

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Not AvailableThe crystal structure of a recombinant triosephosphate isomerase (TIM) from the archaeabacterium Methanocaldococcus jannaschii has been determined at a resolution of 2.3 A using X-ray diffraction data from a tetartohedrally twinned crystal. M. jannaschii TIM (MjTIM) is tetrameric, as suggested by solution studies and from the crystal structure, as is the case for two other structurally characterized archaeal TIMs. The archaeabacterial TIMs are shorter compared with the dimeric TIMs; the insertions in the dimeric TIMs occur in the vicinity of the tetramer interface, resulting in a hindrance to tetramerization in the dimeric TIMs. The charge distribution on the surface of the archaeal TIMs also facilitates tetramerization. Analysis of the barrel interactions in TIMs suggests that these interactions are unlikely to account for the thermal stability of the archaeal TIMs. A novelty of the unliganded structure of MjTIM is the complete absence of electron density for the loop 6 residues. The disorder of this loop could be ascribed to a missing salt bridge between residues at the N- and C-terminal ends of the loop in MjTIM.Not Availabl

Crystal Structures of SCP2 Thiolases of Trypanosomatidae, Human Pathogens Causing Widespread Tropical Diseases The Importance for Catalysis of the Cysteine of the Unique Hdcf Loop.

Thiolases are essential CoA-dependent enzymes in lipid metabolism. In the present study we report the crystal structures of trypanosomal and leishmanial SCP2 (sterol carrier protein, type-2)-thiolases. Trypanosomatidae cause various widespread devastating (sub)-tropical diseases, for which adequate treatment is lacking. The structures reveal the unique geometry of the active site of this poorly characterized subfamily of thiolases. The key catalytic residues of the classical thiolases are two cysteine residues, functioning as a nucleophile and an acid/base respectively. The latter cysteine residue is part of a CxG motif. Interestingly, this cysteine residue is not conserved in SCP2-thiolases. The structural comparisons now show that in SCP2-thiolases the catalytic acid/base is provided by the cysteine residue of the HDCF motif, which is unique for this thiolase subfamily. This HDCF cysteine residue is spatially equivalent to the CxG cysteine residue of classical thiolases. The HDCF cysteine residue is activated for acid/base catalysis by two main chain NH-atoms, instead of two water molecules, as present in the CxG active site. The structural results have been complemented with enzyme activity data, confirming the importance of the HDCF cysteine residue for catalysis. The data obtained suggest that these trypanosomatid SCP2-thiolases are biosynthetic thiolases. These findings provide promise for drug discovery as biosynthetic thiolases catalyse the first step of the sterol biosynthesis pathway that is essential in several of these parasites.</jats:p