scholarly journals Structural and functional analyses of the N-terminal domain of the A subunit of aBacillus megateriumspore germinant receptor

2019 ◽  
Vol 116 (23) ◽  
pp. 11470-11479 ◽  
Author(s):  
Yunfeng Li ◽  
Kai Jin ◽  
Abigail Perez-Valdespino ◽  
Kyle Federkiewicz ◽  
Andrew Davis ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Abc Transporters ◽  
Spore Germination ◽  
Critical Role ◽  
Chemical Shift Perturbation ◽  
Terminal Domain ◽  
Proposed Model ◽  
Strong Homology ◽  
A Subunit ◽  
Functional Analyses

Germination ofBacillusspores is induced by the interaction of specific nutrient molecules with germinant receptors (GRs) localized in the spore’s inner membrane. GRs typically consist of three subunits referred to as A, B, and C, although functions of individual subunits are not known. Here we present the crystal structure of the N-terminal domain (NTD) of the A subunit of theBacillus megateriumGerK3GR, revealing two distinct globular subdomains bisected by a cleft, a fold with strong homology to substrate-binding proteins in bacterial ABC transporters. Molecular docking, chemical shift perturbation measurement, and mutagenesis coupled with spore germination analyses support a proposed model that the interface between the two subdomains in the NTD of GR A subunits serves as the germinant binding site and plays a critical role in spore germination. Our findings provide a conceptual framework for understanding the germinant recruitment mechanism by which GRs trigger spore germination.

scholarly journals Structural characterization of the N-terminal domain of the Dictyostelium discoideum mitochondrial calcium uniporter

2019 ◽  
Author(s):  
Yuan Yuan ◽  
Chan Cao ◽  
Maorong Wen ◽  
Min Li ◽  
Ying Dong ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dictyostelium Discoideum ◽  
Self Assembly ◽  
Calcium Influx ◽  
Transmembrane Protein ◽  
Critical Role ◽  
Mitochondrial Calcium ◽  
Mitochondrial Calcium Uniporter ◽  
Terminal Domain ◽  
Calcium Uniporter

AbstractThe mitochondrial calcium uniporter (MCU) plays a critical role in the mitochondrial calcium uptake into the matrix. In metazoans, the uniporter is a tightly regulated multi-component system including the pore-forming subunit MCU and several regulators (MICU1, MICU2, EMRE). The calcium-conducting activity of metazoan MCU requires the single-transmembrane protein EMRE. Dictyostelium discoideum (Dd), however, developed a simplified uniporter for which the pore-forming MCU (DdMCU) alone is necessary and sufficient for calcium influx. Here, we report a crystal structure of the N-terminal domain (NTD) of DdMCU at 1.7 Å resolution. The DdMCU-NTD contains four helices and two strands arranged in a fold that is completely different from the known structures of other MCU-NTD homologs. Biochemical and biophysical analyses of DdMCU-NTD in solution indicated that the domain exists as oligomers, most probably as a pentamer or hexamer. Mutagenesis showed that the acidic residues Asp60, Glu72 and Glu74, which appeared to mediate the parallel interface as observed in the crystal structure, participated in the self-assembly of DdMCU-NTD. Intriguingly, the oligomeric complex readily dissociated to lower-order oligomers in the presence of calcium. We propose that the calcium-triggered dissociation of NTD regulates the channel activity of DdMCU by a yet unknown mechanism.

scholarly journals Crystal structure of Mycobacterium tuberculosis FadB2 implicated in mycobacterial β-oxidation

2019 ◽  
Vol 75 (1) ◽  
pp. 101-108 ◽  
Author(s):  
Jonathan A. G. Cox ◽  
Rebecca C. Taylor ◽  
Alistair K. Brown ◽  
Samuel Attoe ◽  
Gurdyal S. Besra ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
Critical Role ◽  
Structural Features ◽  
Free Form ◽  
Cofactor Binding ◽  
Terminal Domain ◽  
Hydroxyacyl Coa Dehydrogenase ◽  
Self Association ◽  
Human Orthologue

The intracellular pathogen Mycobacterium tuberculosis is the causative agent of tuberculosis, which is a leading cause of mortality worldwide. The survival of M. tuberculosis in host macrophages through long-lasting periods of persistence depends, in part, on breaking down host cell lipids as a carbon source. The critical role of fatty-acid catabolism in this organism is underscored by the extensive redundancy of the genes implicated in β-oxidation (∼100 genes). In a previous study, the enzymology of the M. tuberculosis L-3-hydroxyacyl-CoA dehydrogenase FadB2 was characterized. Here, the crystal structure of this enzyme in a ligand-free form is reported at 2.1 Å resolution. FadB2 crystallized as a dimer with three unique dimer copies per asymmetric unit. The structure of the monomer reveals a dual Rossmann-fold motif in the N-terminal domain, while the helical C-terminal domain mediates dimer formation. Comparison with the CoA- and NAD+-bound human orthologue mitochondrial hydroxyacyl-CoA dehydrogenase shows extensive conservation of the residues that mediate substrate and cofactor binding. Superposition with the multi-catalytic homologue M. tuberculosis FadB, which forms a trifunctional complex with the thiolase FadA, indicates that FadB has developed structural features that prevent its self-association as a dimer. Conversely, FadB2 is unable to substitute for FadB in the tetrameric FadA–FadB complex as it lacks the N-terminal hydratase domain of FadB. Instead, FadB2 may functionally (or physically) associate with the enoyl-CoA hydratase EchA8 and the thiolases FadA2, FadA3, FadA4 or FadA6 as suggested by interrogation of the STRING protein-network database.

Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1

2019 ◽  
Vol 476 (21) ◽  
pp. 3227-3240 ◽  
Author(s):  
Shanshan Wang ◽  
Yanxiang Zhao ◽  
Long Yi ◽  
Minghe Shen ◽  
Chao Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Conformational Changes ◽  
Magnaporthe Oryzae ◽  
Structural Information ◽  
Complex Structure ◽  
Critical Role ◽  
Catalytic Process ◽  
Structural Basis ◽  
Salt Bridges ◽  
Terminal Domain

Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3–β4 loop to α0 helix) and movement of a ‘shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a ‘closed' state compared with its ‘open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.

scholarly journals Catalytic effectiveness of human aldose reductase. Critical role of C-terminal domain.

1992 ◽  
Vol 267 (29) ◽  
pp. 20965-20970
Author(s):  
K.M. Bohren ◽  
C.E. Grimshaw ◽  
K.H. Gabbay
Keyword(s):  
Aldose Reductase ◽  
Critical Role ◽  
Terminal Domain

scholarly journals Author Correction: Crystal structure of Type IX secretion system PorE C-terminal domain from Porphyromonas gingivalis in complex with a peptidoglycan fragment

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nhung Thi Trang Trinh ◽  
Hieu Quang Tran ◽  
Quyen Van Dong ◽  
Christian Cambillau ◽  
Alain Roussel ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Porphyromonas Gingivalis ◽  
Secretion System ◽  
Terminal Domain ◽  
Type Ix Secretion System

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

scholarly journals Graph contextualized attention network for predicting synthetic lethality in human cancers

2021 ◽  
Author(s):  
Yahui Long ◽  
Min Wu ◽  
Yong Liu ◽  
Jie Zheng ◽  
Chee Keong Kwoh ◽  
...  
Keyword(s):  
Synthetic Lethality ◽  
Critical Role ◽  
Design Feature ◽  
Cost Effective ◽  
Attention Network ◽  
New Genes ◽  
Lab Experiments ◽  
Proposed Model ◽  
Multiple Feature ◽  
Wet Lab

Abstract Motivation Synthetic Lethality (SL) plays an increasingly critical role in the targeted anticancer therapeutics. In addition, identifying SL interactions can create opportunities to selectively kill cancer cells without harming normal cells. Given the high cost of wet-lab experiments, in silico prediction of SL interactions as an alternative can be a rapid and cost-effective way to guide the experimental screening of candidate SL pairs. Several matrix factorization-based methods have recently been proposed for human SL prediction. However, they are limited in capturing the dependencies of neighbors. In addition, it is also highly challenging to make accurate predictions for new genes without any known SL partners. Results In this work, we propose a novel graph contextualized attention network named GCATSL to learn gene representations for SL prediction. First, we leverage different data sources to construct multiple feature graphs for genes, which serve as the feature inputs for our GCATSL method. Second, for each feature graph, we design node-level attention mechanism to effectively capture the importance of local and global neighbors and learn local and global representations for the nodes, respectively. We further exploit multi-layer perceptron (MLP) to aggregate the original features with the local and global representations and then derive the feature-specific representations. Third, to derive the final representations, we design feature-level attention to integrate feature-specific representations by taking the importance of different feature graphs into account. Extensive experimental results on three datasets under different settings demonstrated that our GCATSL model outperforms 14 state-of-the-art methods consistently. In addition, case studies further validated the effectiveness of our proposed model in identifying novel SL pairs. Availability Python codes and dataset are freely available on GitHub (https://github.com/longyahui/GCATSL) and Zenodo (https://zenodo.org/record/4522679) under the MIT license.

scholarly journals Serendipitous crystallization and structure determination of bacterioferritin from Achromobacter

2018 ◽  
Vol 74 (9) ◽  
pp. 558-566
Author(s):  
Abhisek Dwivedy ◽  
Bhavya Jha ◽  
Khundrakpam Herojit Singh ◽  
Mohammed Ahmad ◽  
Anam Ashraf ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Iron Homeostasis ◽  
Critical Role ◽  
Porphyrin Ring ◽  
Opportunistic Pathogens ◽  
Complex Design ◽  
Archaeal Species ◽  
Ferroxidase Center ◽  
Mycobacterial Protein

Bacterioferritins (Bfrs) are ferritin-like molecules with a hollow spherical 24-mer complex design that are unique to bacterial and archaeal species. They play a critical role in storing iron(III) within the complex at concentrations much higher than the feasible solubility limits of iron(III), thus maintaining iron homeostasis within cells. Here, the crystal structure of bacterioferritin from Achromobacter (Ach Bfr) that crystallized serendipitously during a crystallization attempt of an unrelated mycobacterial protein is reported at 1.95 Å resolution. Notably, Fe atoms were bound to the structure along with a porphyrin ring sandwiched between the subunits of a dimer. Furthermore, the dinuclear ferroxidase center of Ach Bfr has only a single iron bound, in contrast to the two Fe atoms in other Bfrs. The structure of Ach Bfr clearly demonstrates the substitution of a glutamate residue, which is involved in the interaction with the second Fe atom, by a threonine and the consequent absence of another Fe atom there. The iron at the dinuclear center has a tetravalent coordination, while a second iron with a hexavalent coordination was found within the porphyrin ring, generating a heme moiety. Achromobacter spp. are known opportunistic pathogens; this structure enhances the current understanding of their iron metabolism and regulation, and importantly will be useful in the design of small-molecule inhibitors against this protein through a structure-guided approach.

Sign in / Sign up

Export Citation Format

Share Document