scholarly journals An alternative domain-swapped structure of the Pyrococcus horikoshii PolII mini-intein

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jennie E. Williams ◽  
Mario V. Jaramillo ◽  
Zhong Li ◽  
Jing Zhao ◽  
Chunyu Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Activity ◽  
Active Site ◽  
Homing Endonuclease ◽  
Protein Splicing ◽  
Pyrococcus Horikoshii ◽  
Linker Region ◽  
Higher Temperature ◽  
Pyrococcus Abyssi ◽  
Translational Process

AbstractProtein splicing is a post-translational process by which an intein catalyzes its own excision from flanking polypeptides, or exteins, concomitant with extein ligation. Many inteins have nested homing endonuclease domains that facilitate their propagation into intein-less alleles, whereas other inteins lack the homing endonuclease (HEN) and are called mini-inteins. The mini-intein that interrupts the DNA PolII of Pyrococcus horikoshii has a linker region in place of the HEN domain that is shorter than the linker in a closely related intein from Pyrococcus abyssi. The P. horikoshii PolII intein requires a higher temperature for catalytic activity and is more stable to digestion by the thermostable protease thermolysin, suggesting that it is more rigid than the P. abyssi intein. We solved a crystal structure of the intein precursor that revealed a domain-swapped dimer. Inteins found as domain swapped dimers have been shown to promote intein-mediated protein alternative splicing, but the solved P. horikoshii PolII intein structure has an active site unlikely to be catalytically competent.

scholarly journals 3-D Structure of Serum Paraoxonase 1 Sheds Light on Its Activity, Stability, Solubility and Crystallizability

2007 ◽  
Vol 58 (3) ◽  
pp. 347-353 ◽  
Author(s):  
Michal Harel ◽  
Boris Brumshtein ◽  
Ran Meged ◽  
Hay Dvir ◽  
Raimond Ravelli ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Activity ◽  
High Density Lipoprotein ◽  
Active Site ◽  
Density Lipoprotein ◽  
Paraoxonase 1 ◽  
Hydrolytic Activities ◽  
Wide Range ◽  
The Stability ◽  
Serum Paraoxonase

3-D Structure of Serum Paraoxonase 1 Sheds Light on Its Activity, Stability, Solubility and CrystallizabilitySerum paraoxonases (PONs) exhibit a wide range of physiologically important hydrolytic activities, including drug metabolism and detoxification of nerve gases. PON1 and PON3 reside on high-density lipoprotein (HDL) (the "good cholesterol"), and are involved in the alleviation of atherosclerosis. Members of the PON family have been identified not only in mammals and other vertebrates, but also in invertebrates. We earlier described the first crystal structure of a PON family member, a directly-evolved variant of PON1, at 2.2 Å resolution. PON1 is a 6-bladed beta-propeller with a unique active-site lid which is also involved in binding to HDL. The 3-D structure, taken together with directed evolution studies, permitted analysis of mutations which enhanced the stability, solubility and crystallizability of this PON1 variant. The structure permits a detailed description of PON1's active site and suggests possible mechanisms for its catalytic activity on certain substrates.

scholarly journals Crystal Structure of PI-SceI, a Homing Endonuclease with Protein Splicing Activity

Cell ◽  
1997 ◽  
Vol 89 (4) ◽  
pp. 555-564 ◽  
Author(s):  
Xiaoqun Duan ◽  
Frederick S Gimble ◽  
Florante A Quiocho
Keyword(s):  
Crystal Structure ◽  
Homing Endonuclease ◽  
Protein Splicing

scholarly journals Interaction of novel oxazoline derivatives of 17(20)e-pregna-5,17(20)-diene with cytochrome P450 17A1

2016 ◽  
Vol 62 (1) ◽  
pp. 38-44 ◽  
Author(s):  
S.V. Stulov ◽  
N.O. Dugin ◽  
M.S. Zharkova ◽  
D.S. Shcherbinin ◽  
A.V. Kuzikov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cytochrome P450 ◽  
Catalytic Activity ◽  
Molecular Docking ◽  
Complex Formation ◽  
Active Site ◽  
Heme Iron ◽  
New Drugs ◽  
Key Enzyme ◽  
Derivatives Of

In order to find novel inhibitors of 17a-hydroxylase-17,20-lyase (cytochrome P450 17A1, CYP17A1), a key enzyme of biosynthesis of androgens, molecular docking of six new oxazoline-containing derivatives 17(20)E-pregna-5,17(20)-diene has been carried out to the active site of the crystal structure of CYP17A1 (pdb 3ruk). Results of this study indicate that: 1) complex formation of docked compounds with CYP17A1 causes their isomerization in energetically less favorable 17(20)Z-isomer; 2) the localization of the steroid moiety of all compounds in the active site is basically the same; 3) the structure of the oxazoline moiety significantly influences its position relative to heme as well as the energy of complex formation; 4) coordination of the nitrogen atom of the oxazoline moiety and the heme iron is only possible in the 17(20)Z-conformation with anti oriented double bonds 17(20), and C=N; 5) the presence of two substituents at C4' of the oxazoline moiety significantly impairs ligand binding; 6) oxazoline - and benzoxazole-containing derivatives 17(20)E-pregna-5,17(20)-diene can effectively inhibit the catalytic activity CYP17A1 and may be of interest as a basis for the development of new drugs for the treatment of androgen-dependent cancer.

scholarly journals Evaluation of the role of two conserved active-site residues in Beta class glutathione S-transferases

2000 ◽  
Vol 351 (2) ◽  
pp. 341-346 ◽  
Author(s):  
Nerino ALLOCATI ◽  
Enrico CASALONE ◽  
Michele MASULLI ◽  
Galina POLEKHINA ◽  
Jamie ROSSJOHN ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thermal Stability ◽  
Catalytic Activity ◽  
Proteus Mirabilis ◽  
Active Site ◽  
Binding Capacity ◽  
Active Site Residues ◽  
Terminal Domain ◽  
Glutathione S Transferases

Glutathione S-transferases (GSTs) normally use hydroxy-group-containing residues in the N-terminal domain of the enzyme for stabilizing the activated form of the co-substrate, glutathione. However, previous mutagenesis studies have shown that this is not true for Beta class GSTs and thus the origin of the stabilization remains a mystery. The recently determined crystal structure of Proteus mirabilis GST B1-1 (PmGST B1-1) suggested that the stabilizing role might be fulfilled in Beta class GSTs by one or more residues in the C-terminal domain of the enzyme. To test this hypothesis we mutated His106 and Lys107 of PmGST B1-1 to investigate their possible role in the enzyme's catalytic activity. His106 was mutated to Ala, Asn and Phe, and Lys107 to Ala and Arg. The effects of the replacement on the activity, thermal stability and antibiotic-binding capacity of the enzyme were examined. The results are consistent with the involvement of His106 and Lys107 in interacting with glutathione at the active site but these residues do not contribute significantly to catalysis, folding or antibiotic binding.

scholarly journals Flower-Shaped C-Dots/Co3O4{111} Constructed with Dual-Reaction Centers for Enhancement of Fenton-Like Reaction Activity and Peroxymonosulfate Conversion to Sulfate Radical

Catalysts ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 135
Author(s):  
Zhibin Wen ◽  
Qianqian Zhu ◽  
Jiali Zhou ◽  
Shudi Zhao ◽  
Jinnan Wang ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Active Site ◽  
High Surface ◽  
High Surface Area ◽  
Reaction Centers ◽  
Organic Radicals ◽  
The Other ◽  
High Catalytic Activity ◽  
High Adsorption ◽  
High Turnover

Novel flower-shaped C-dots/Co3O4{111} with dual-reaction centers were constructed to improve the Fenton-like reaction activity and peroxymonosulfate (PMS) conversion to sulfate radicals. Due to the exposure of a high surface area and Co3O4{111} facets, flower-shaped C-dots/Co3O4{111} could provide more Co(II) for PMS activation than traditional spherical Co3O4{110}. Meanwhile, PMS was preferred for adsorption on Co3O4{111} facets because of a high adsorption energy and thereby facilitated the electron transfer from Co(II) to PMS. More importantly, the Co–O–C linkage between C-dots and Co3O4{111} induced the formation of the dual-reaction center, which promoted the production of reactive organic radicals (R•). PMS could be directly reduced to SO4−• by R• over C-dots. On the other hand, electron transferred from R• to Co via Co–O–C linkage could accelerate the redox of Co(II)/(III), avoiding the invalid decomposition of PMS. Thus, C-dots doped on Co3O4{111} improved the PMS conversion rate to SO4−• over the single active site, resulting in high turnover numbers (TONs). In addition, TPR analysis indicated that the optimal content of C-dots doped on Co3O4{111} is 2.5%. More than 99% of antibiotics and dyes were degraded over C-dots/Co3O4{111} within 10 min. Even after six cycles, C-dots/Co3O4{111} still remained a high catalytic activity.

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