Structural basis for the mechanisms of human presequence protease conformational switch and substrate recognition

Abstract Presequence protease (PreP), a 117 kDa mitochondrial M16C metalloprotease vital for mitochondrial proteostasis, degrades presequence peptides cleaved off from nuclear-encoded proteins and other aggregation-prone peptides, such as amyloid β (Aβ). PreP structures have only been determined in a closed conformation; thus, the mechanisms of substrate binding and selectivity remain elusive. Here, we leverage advanced vitrification techniques to overcome the preferential denaturation of one of two ~55 kDa homologous domains of PreP caused by air-water interface adsorption, and thereby elucidate cryoEM structures of three apo-PreP open states along with Aβ- and citrate synthase presequence-bound PreP at 3.3 Å-4.6 Å resolution. Together with integrative biophysical and pharmacological approaches, these structures reveal the key stages of the PreP catalytic cycle and how the binding of substrates or PreP inhibitor drives the rigid body motion of the protein for substrate binding and catalysis. Together, our studies provide key mechanistic insights into M16C metalloproteases for future therapeutic innovations.

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Structural basis of substrate recognition and translocation by human ABCA4

10.1101/2021.02.27.433154 ◽

2021 ◽

Author(s):

Tian Xie ◽

Zike Zhang ◽

Bowen Du ◽

Qi Fang ◽

Xin Gong

Keyword(s):

Substrate Recognition ◽

Bound State ◽

Lipid Transport ◽

Structural Basis ◽

Lateral Entry ◽

Closed Conformation ◽

Hereditary Disorders ◽

Extrusion Mechanism ◽

Functional States ◽

Lipid Compounds

AbstractHuman ATP-binding cassette (ABC) subfamily A (ABCA) transporters mediate the transport of various lipid compounds across the membrane. Mutations in human ABCA transporters have been described to cause severe hereditary disorders associated with impaired lipid transport. However, little is known about the mechanistic details of substrate recognition and translocation by ABCA transporters. Here, we present three cryo-EM structures of human ABCA4, a retinal-specific ABCA transporter, in distinct functional states at resolutions of 3.3-3.4 Å. In the nucleotide-free state, the two transmembrane domains (TMDs) exhibited a lateral-opening conformation, allowing the lateral entry of substrate from the lipid bilayer. N-retinylidene-phosphatidylethanolamine (NRPE), the physiological lipid substrate of ABCA4, is sandwiched between the two TMDs in the luminal leaflet and is further stabilized by an extended loop from extracellular domain 1. In the ATP-bound state, the two TMDs displayed an unprecedented closed conformation, which precludes the substrate binding. Our study provides a molecular basis to understand the mechanism of ABCA4-mediated NRPE recognition and translocation, and suggests a common ‘lateral access and extrusion’ mechanism for ABCA-mediated lipid transport.

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Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2020.02.146 ◽

2020 ◽

Vol 525 (3) ◽

pp. 720-725

Author(s):

Kaho Shimamura ◽

Tomonori Akiyama ◽

Kazuhiro Yokoyama ◽

Mihoko Takenoya ◽

Shinsaku Ito ◽

...

Keyword(s):

Binding Protein ◽

Substrate Binding ◽

Substrate Recognition ◽

Structural Basis ◽

Substrate Binding Protein ◽

Microbacterium Hydrocarbonoxydans

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Cap-domain closure enables diverse substrate recognition by the C2-type haloacid dehalogenase-like sugar phosphatasePlasmodium falciparumHAD1

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004715012067 ◽

2015 ◽

Vol 71 (9) ◽

pp. 1824-1834 ◽

Cited By ~ 7

Author(s):

Jooyoung Park ◽

Ann M. Guggisberg ◽

Audrey R. Odom ◽

Niraj H. Tolia

Keyword(s):

Structural Changes ◽

Substrate Binding ◽

Substrate Recognition ◽

Structural Basis ◽

Structural Determinants ◽

Biochemical Basis ◽

Multiple Substrates ◽

Methylerythritol Phosphate ◽

Enzyme Superfamily ◽

Sugar Phosphates

Haloacid dehalogenases (HADs) are a large enzyme superfamily of more than 500 000 members with roles in numerous metabolic pathways.Plasmodium falciparumHAD1 (PfHAD1) is a sugar phosphatase that regulates the methylerythritol phosphate (MEP) pathway for isoprenoid synthesis in malaria parasites. However, the structural determinants for diverse substrate recognition by HADs are unknown. Here, crystal structures were determined of PfHAD1 in complex with three sugar phosphates selected from a panel of diverse substrates that it utilizes. Cap-open and cap-closed conformations are observed, with cap closure facilitating substrate binding and ordering. These structural changes define the role of cap movement within the major subcategory of C2 HAD enzymes. The structures of an HAD bound to multiple substrates identifies binding and specificity-determining residues that define the structural basis for substrate recognition and catalysis within the HAD superfamily. While the substrate-binding region of the cap domain is flexible in the open conformations, this region becomes ordered and makes direct interactions with the substrate in the closed conformations. These studies further inform the structural and biochemical basis for catalysis within a large superfamily of HAD enzymes with diverse functions.

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Structural basis of substrate recognition and translocation by human ABCA4

Nature Communications ◽

10.1038/s41467-021-24194-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Tian Xie ◽

Zike Zhang ◽

Qi Fang ◽

Bowen Du ◽

Xin Gong

Keyword(s):

Substrate Recognition ◽

Bound State ◽

Lipid Transport ◽

Structural Basis ◽

Lateral Entry ◽

Closed Conformation ◽

Hereditary Disorders ◽

Extrusion Mechanism ◽

Functional States ◽

Lipid Compounds

AbstractHuman ATP-binding cassette (ABC) subfamily A (ABCA) transporters mediate the transport of various lipid compounds across the membrane. Mutations in human ABCA transporters have been described to cause severe hereditary disorders associated with impaired lipid transport. However, little is known about the mechanistic details of substrate recognition and translocation by ABCA transporters. Here, we present three cryo-EM structures of human ABCA4, a retina-specific ABCA transporter, in distinct functional states at resolutions of 3.3–3.4 Å. In the nucleotide-free state, the two transmembrane domains (TMDs) exhibit a lateral-opening conformation, allowing the lateral entry of substrate from the lipid bilayer. The N-retinylidene-phosphatidylethanolamine (NRPE), the physiological lipid substrate of ABCA4, is sandwiched between the two TMDs in the luminal leaflet and is further stabilized by an extended loop from extracellular domain 1. In the ATP-bound state, the two TMDs display a closed conformation, which precludes the substrate binding. Our study provides a molecular basis to understand the mechanism of ABCA4-mediated NRPE recognition and translocation, and suggests a common ‘lateral access and extrusion’ mechanism for ABCA-mediated lipid transport.

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Schisandrin Restores the Amyloid β-Induced Impairments on Mitochondrial Function, Energy Metabolism, Biogenesis, and Dynamics in Rat Primary Hippocampal Neurons

Pharmacology ◽

10.1159/000507818 ◽

2021 ◽

pp. 1-11

Author(s):

Zhongyuan Piao ◽

Lin Song ◽

Lifen Yao ◽

Limei Zhang ◽

Yichan Lu

Keyword(s):

Energy Metabolism ◽

Cytochrome C ◽

Mitochondrial Biogenesis ◽

Mitochondrial Function ◽

Hippocampal Neurons ◽

Citrate Synthase ◽

Mitochondrial Permeability Transition ◽

Amyloid Β ◽

Mitochondrial Functions ◽

Primary Hippocampal Neurons

Introduction: Schisandrin which is derived from Schisandra chinensis has shown multiple pharmacological effects on various diseases including Alzheimer’s disease (AD). It is demonstrated that mitochondrial dysfunction plays an essential role in the pathogenesis of neurodegenerative disorders. Objective: Our study aims to investigate the effects of schisandrin on mitochondrial functions and metabolisms in primary hippocampal neurons. Methods: In our study, rat primary hippocampal neurons were isolated and treated with indicated dose of amyloid β1–42 (Aβ1–42) oligomer to establish a cell model of AD in vitro. Schisandrin (2 μg/mL) was further subjected to test its effects on mitochondrial function, energy metabolism, mitochondrial biogenesis, and dynamics in the Aβ1–42 oligomer-treated neurons. Results and Conclusions: Our findings indicated that schisandrin significantly alleviated the Aβ1–42 oligomer-induced loss of mitochondrial membrane potential and impaired cytochrome c oxidase activity. Additionally, the opening of mitochondrial permeability transition pore and release of cytochrome c were highly restricted with schisandrin treatment. Alterations in cell viability, ATP production, citrate synthase activity, and the expressions of glycolysis-related enzymes demonstrated the relief of defective energy metabolism in Aβ-treated neurons after the treatment of schisandrin. For mitochondrial biogenesis, elevated expression of peroxisome proliferator-activated receptor γ coactivator along with promoted mitochondrial mass was found in schisandrin-treated cells. The imbalance in the cycle of fusion and fission was also remarkably restored by schisandrin. In summary, this study provides novel mechanisms for the protective effect of schisandrin on mitochondria-related functions.

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Structural and Functional Insights into Peptidoglycan Access for the Lytic Amidase LytA of Streptococcus pneumoniae

mBio ◽

10.1128/mbio.01120-13 ◽

2014 ◽

Vol 5 (1) ◽

Cited By ~ 31

Author(s):

Peter Mellroth ◽

Tatyana Sandalova ◽

Alexey Kikhney ◽

Francisco Vilaplana ◽

Dusan Hesek ◽

...

Keyword(s):

Cell Wall ◽

Streptococcus Pneumoniae ◽

Solution Structure ◽

Substrate Binding ◽

Substrate Recognition ◽

Lytic Activity ◽

Site Directed Mutagenesis ◽

Binding Motif ◽

Content Type ◽

Peptidoglycan Synthesis

ABSTRACT The cytosolic N-acetylmuramoyl-l-alanine amidase LytA protein of Streptococcus pneumoniae, which is released by bacterial lysis, associates with the cell wall via its choline-binding motif. During exponential growth, LytA accesses its peptidoglycan substrate to cause lysis only when nascent peptidoglycan synthesis is stalled by nutrient starvation or β-lactam antibiotics. Here we present three-dimensional structures of LytA and establish the requirements for substrate binding and catalytic activity. The solution structure of the full-length LytA dimer reveals a peculiar fold, with the choline-binding domains forming a rigid V-shaped scaffold and the relatively more flexible amidase domains attached in a trans position. The 1.05-Å crystal structure of the amidase domain reveals a prominent Y-shaped binding crevice composed of three contiguous subregions, with a zinc-containing active site localized at the bottom of the branch point. Site-directed mutagenesis was employed to identify catalytic residues and to investigate the relative impact of potential substrate-interacting residues lining the binding crevice for the lytic activity of LytA. In vitro activity assays using defined muropeptide substrates reveal that LytA utilizes a large substrate recognition interface and requires large muropeptide substrates with several connected saccharides that interact with all subregions of the binding crevice for catalysis. We hypothesize that the substrate requirements restrict LytA to the sites on the cell wall where nascent peptidoglycan synthesis occurs. IMPORTANCE Streptococcus pneumoniae is a human respiratory tract pathogen responsible for millions of deaths annually. Its major pneumococcal autolysin, LytA, is required for autolysis and fratricidal lysis and functions as a virulence factor that facilitates the spread of toxins and factors involved in immune evasion. LytA is also activated by penicillin and vancomycin and is responsible for the lysis induced by these antibiotics. The factors that regulate the lytic activity of LytA are unclear, but it was recently demonstrated that control is at the level of substrate recognition and that LytA required access to the nascent peptidoglycan. The present study was undertaken to structurally and functionally investigate LytA and its substrate-interacting interface and to determine the requirements for substrate recognition and catalysis. Our results reveal that the amidase domain comprises a complex substrate-binding crevice and needs to interact with a large-motif epitope of peptidoglycan for catalysis.

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