scholarly journals Comments on the recent crystal structure of TsaBDE complex of bacterial t6A biosynthesis system and its significance for understanding TC-AMP processing

2019 ◽  
Author(s):  
Boguslaw Stec
Keyword(s):  
Crystal Structure ◽  
Active Sites ◽  
Structural Model ◽  
Thermotoga Maritima ◽  
Biosynthesis Pathway ◽  
Binding Modes ◽  
Anticodon Loop ◽  
Structural Details ◽  
Unstable Intermediate ◽  
Trna Binding

ABSTRACTThe N(6)-threonylcarbamoyl adenosine (t6A) modification at position 37 of a tRNA of the anticodon loop is universal and central to the translational fidelity of all known organisms. The ternary complex of TsaBDE is the central and essential workstation for t6A biosynthesis in bacteria. The recently published crystal structure of Thermotoga maritima (T.maritima) TsaBDE complex (Missoury et al., 2018) has ~15% incorrectly-placed, misplaced/mistraced, or missing residues. These structural errors have precipitated incorrect conclusions about the disordering of the active site and inferred action of the TsaE element. In this report, we rectify the published structural model of the T.maritima TsaBDE complex. In stark contrast, a corrected structural model of TsaBDE shows that both active sites of the TsaD element are fully occupied with threonylcarbamoyladenosine (TC-AMP), an unstable intermediate chemical moiety of the t6A biosynthesis pathway. This observation has profound implications for understanding the funneling of intermediates in the t6A pathway and also in helping to elucidate tRNA binding modes. Based on the structural details described in here we propose a unifying principle for binding the tRNA to the TsaD subunit of the complex which is universally required in all known t6A modification pathways.

scholarly journals Chemical IN04 Inhibits the Kinase Domain not the ROC Domain of LRRK1: Results from Homology Modeling and Molecular Docking

2020 ◽  
Vol 16 ◽  
Author(s):  
Zhenhang Chen ◽  
Weirong Xing ◽  
Li Fan
Keyword(s):  
Bone Loss ◽  
Active Site ◽  
Active Sites ◽  
Structural Model ◽  
Osteoporotic Fractures ◽  
Salt Bridge ◽  
Homology Model ◽  
The Elderly ◽  
Kinase Domain ◽  
Binding Modes

Background: Bone loss is the most common reason for broken bones among the elderly. An ideal agent for treatment of bone loss should have both osteoclast inhibitory and osteoblast stimulatory functions. Leucine rich repeat kinase 1 (LRRK1) is a novel target for alternative anti-resorptive drugs to treat osteoporosis and osteoporotic fractures. Recently a chemical IN04, Methyl 3-[(([5-(3,5-dimethoxyphenyl)-1,3,4-oxadiazol-2-yl]-thio-acetyl)-amino]-benzoate, has been identified as a potential LRRK1 inhibitor. Objective: The aim of this work is to investigate how the chemical IN04 interacts with LRRK1 and inhibits its activity. Methods: A structural model of LRRK1 kinase domain was constructed with SWISS-MODEL. The human protein kinase ROCO4 (PDB ID: 4YZN) was chosen as the template based on sequence homology, structural and phylogenetic analysis. In addition, a homology model of the LRRK1 ROC domain was also prepared based on the LRRK2 ROC domain structure (PDB ID: 2ZEJ). The interactions of IN04 with the active sites in the LRRK1 kinase domain and ROC domain were investigated by SwissDock. Results: IN04 was docked into the active site of the LRRK1 kinase domain with similar interactions as ATP comparable to the ligand bound to homologous kinases. Many rational binding modes of IN04 to LRRK1 kinase domain were investigated and the most likely binding pose containing multiple hydrogen bonds and a salt bridge was discovered. However, IN04 cannot fit into the GDP-binding site of the ROC domain. Conclusion: Chemical IN04 inhibits LRRK1 by binding to the active site of the kinase domain but not the ROC domain.

scholarly journals Comparative Analysis of the Escherichia coli Ketopantoate Hydroxymethyltransferase Crystal Structure Confirms that It Is a Member of the (βα)8 Phosphoenolpyruvate/Pyruvate Superfamily

2003 ◽  
Vol 185 (14) ◽  
pp. 4163-4171 ◽  
Author(s):  
Florian Schmitzberger ◽  
Alison G. Smith ◽  
Chris Abell ◽  
Tom L. Blundell
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Comparative Analysis ◽  
Structural Analysis ◽  
Active Sites ◽  
Vitamin B ◽  
Biosynthesis Pathway ◽  
Hydroxymethyl Group ◽  
E Coli ◽  
Structural Homologues

ABSTRACT Escherichia coli ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first step in the biosynthesis pathway of pantothenate (vitamin B5), the transfer of a hydroxymethyl group onto α-ketoisovalerate. Here we describe a detailed comparative analysis of the KPHMT crystal structure and the identification of structural homologues, some of which have remarkable similarities in their active sites, modes of binding to substrates, and mechanisms. We show that KPHMT forms a family within the phosphoenolpyruvate/pyruvate superfamily. Based on the analysis, we propose that in this superfamily there should be a subdivision into two groups. This paper completes our structural analysis of the E. coli enzymes in the pantothenate pathway.

On the Adsorption of Aspartate Derivatives to Calcite Surfaces in Aqueous Environment

2020 ◽  
Author(s):  
Robert Stepic ◽  
Lara Jurković ◽  
Ksenia Klementyeva ◽  
Marko Ukrainczyk ◽  
Matija Gredičak ◽  
...  
Keyword(s):  
Active Sites ◽  
Realistic Model ◽  
Binding Energies ◽  
Inhibition Mechanism ◽  
Aqueous Environment ◽  
Binding Modes ◽  
Carboxylate Groups ◽  
Dissolved Ions ◽  
Living Organisms ◽  
Dynamics Simulations

In many living organisms, biomolecules interact favorably with various surfaces of calcium carbonate. In this work, we have considered the interactions of aspartate (Asp) derivatives, as models of complex biomolecules, with calcite. Using kinetic growth experiments, we have investigated the inhibition of calcite growth by Asp, Asp2 and Asp3.This entailed the determination of a step-pinning growth regime as well as the evaluation of the adsorption constants and binding free energies for the three species to calcite crystals. These latter values are compared to free energy profiles obtained from fully atomistic molecular dynamics simulations. When using a flat (104) calcite surface in the models, the measured trend of binding energies is poorly reproduced. However, a more realistic model comprised of a surface with an island containing edges and corners, yields binding energies that compare very well with experiments. Surprisingly, we find that most binding modes involve the positively charged, ammonium group. Moreover, while attachment of the negatively charged carboxylate groups is also frequently observed, it is always balanced by the aqueous solvation of an equal or greater number of carboxylates. These effects are observed on all calcite features including edges and corners, the latter being associated with dominant affinities to Asp derivatives. As these features are also precisely the active sites for crystal growth, the experimental and theoretical results point strongly to a growth inhibition mechanism whereby these sites become blocked, preventing further attachment of dissolved ions and halting further growth.

scholarly journals The RelA hydrolase domain acts as a molecular switch for (p)ppGpp synthesis

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Anurag Kumar Sinha ◽  
Kristoffer Skovbo Winther
Keyword(s):  
Active Sites ◽  
Molecular Switch ◽  
Cell Physiology ◽  
Synthetase Activity ◽  
Wild Type ◽  
Functional Studies ◽  
Loop Region ◽  
A Site ◽  
Trna Binding

AbstractBacteria synthesize guanosine tetra- and penta phosphate (commonly referred to as (p)ppGpp) in response to environmental stresses. (p)ppGpp reprograms cell physiology and is essential for stress survival, virulence and antibiotic tolerance. Proteins of the RSH superfamily (RelA/SpoT Homologues) are ubiquitously distributed and hydrolyze or synthesize (p)ppGpp. Structural studies have suggested that the shift between hydrolysis and synthesis is governed by conformational antagonism between the two active sites in RSHs. RelA proteins of γ-proteobacteria exclusively synthesize (p)ppGpp and encode an inactive pseudo-hydrolase domain. Escherichia coli RelA synthesizes (p)ppGpp in response to amino acid starvation with cognate uncharged tRNA at the ribosomal A-site, however, mechanistic details to the regulation of the enzymatic activity remain elusive. Here, we show a role of the enzymatically inactive hydrolase domain in modulating the activity of the synthetase domain of RelA. Using mutagenesis screening and functional studies, we identify a loop region (residues 114–130) in the hydrolase domain, which controls the synthetase activity. We show that a synthetase-inactive loop mutant of RelA is not affected for tRNA binding, but binds the ribosome less efficiently than wild type RelA. Our data support the model that the hydrolase domain acts as a molecular switch to regulate the synthetase activity.

scholarly journals Threonine 57 is required for the post-translational activation ofEscherichia coliaspartate α-decarboxylase

2014 ◽  
Vol 70 (4) ◽  
pp. 1166-1172 ◽  
Author(s):  
Michael E. Webb ◽  
Briony A. Yorke ◽  
Tom Kershaw ◽  
Sarah Lovelock ◽  
Carina M. C. Lobley ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Site Directed Mutagenesis ◽  
Intramolecular Rearrangement ◽  
Directed Mutagenesis ◽  
Vitamin B ◽  
Biosynthesis Pathway ◽  
Serine Residue ◽  
Translational Activation

Aspartate α-decarboxylase is a pyruvoyl-dependent decarboxylase required for the production of β-alanine in the bacterial pantothenate (vitamin B5) biosynthesis pathway. The pyruvoyl group is formedviathe intramolecular rearrangement of a serine residue to generate a backbone ester intermediate which is cleaved to generate an N-terminal pyruvoyl group. Site-directed mutagenesis of residues adjacent to the active site, including Tyr22, Thr57 and Tyr58, reveals that only mutation of Thr57 leads to changes in the degree of post-translational activation. The crystal structure of the site-directed mutant T57V is consistent with a non-rearranged backbone, supporting the hypothesis that Thr57 is required for the formation of the ester intermediate in activation.

Crystal Structure of Full Length Topoisomerase I from Thermotoga maritima

2006 ◽  
Vol 358 (5) ◽  
pp. 1328-1340 ◽  
Author(s):  
Guido Hansen ◽  
Axel Harrenga ◽  
Bernd Wieland ◽  
Dietmar Schomburg ◽  
Peter Reinemer
Keyword(s):  
Crystal Structure ◽  
Topoisomerase I ◽  
Thermotoga Maritima ◽  
Full Length

The structure and activity of potassium supported on SBA-15 molecular sieve: Density functional theory study

2014 ◽  
Vol 13 (01) ◽  
pp. 1350076 ◽  
Author(s):  
Bing Liu ◽  
Daxi Wang ◽  
Zhongxue Wang ◽  
Zhen Zhao ◽  
Yu Chen ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Lewis Acid ◽  
Molecular Sieve ◽  
Active Sites ◽  
Density Functional ◽  
Structural Model ◽  
Vibrational Frequencies ◽  
Oxygen Molecule ◽  
Lewis Base ◽  
Functional Theory

The geometries, vibrational frequencies, electronic properties and reactivity of potassium supported on SBA-15 have been theoretically investigated by the density functional theory (DFT) method. The structural model of the potassium supported on SBA-15 was constructed based on our previous work [Wang ZX, Wang DX, Zhao Z, Chen Y, Lan J, A DFT study of the structural units in SBA-15 mesoporous molecular sieve, Comput. Theor. Chem.963, 403, 2011]. This paper is the extension of our previous work. The most favored location of potassium atom was obtained by the calculation of substitution energy. The calculated vibrational frequencies of K /SBA-15 are in good agreement with the experimental results. By analyzing the properties of electronic structure, we found that the O atom of Si - O (2)- K group acts as the Lewis base center and the K atom acts as the Lewis acid center. The reactivity of K /SBA-15 was investigated by calculating the activation of oxygen molecule. The oxygen molecule can be activated by K /SBA-15 with an energy barrier of 103.2 kJ/mol. In the final state, the activated oxygen atoms become new Lewis acid centers, which are predicted to act as the active sites in the catalytic reactions. This study provides a deep insight into the properties of supported potassium catalysts and offers fundamental information for further research.

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