scholarly journals Structural basis of self-assembly in the lipid-binding domain of mycobacterial polar growth factor Wag31

IUCrJ ◽  
2020 ◽  
Vol 7 (4) ◽  
pp. 767-776
Author(s):  
Komal Choukate ◽  
Barnali Chaudhuri
Keyword(s):  
Crystal Structure ◽  
Self Assembly ◽  
Membrane Lipids ◽  
Crystal Packing ◽  
Lipid Binding ◽  
Binding Domain ◽  
Size Exclusion ◽  
Scattering Data ◽  
Structural Basis ◽  
Polar Growth

Wag31, or DivIVA, is an essential protein and a drug target in the human pathogen Mycobacterium tuberculosis that self-assembles at the negatively curved membrane surface to form a higher-order structural scaffold, maintains rod-shaped cellular morphology and localizes key cell-wall synthesizing enzymes at the pole for exclusive polar growth. The crystal structure of the N-terminal lipid-binding domain of mycobacterial Wag31 was determined at 2.3 Å resolution. The structure revealed a highly polar surface lined with several conserved charged residues that suggest probable sites for interactions with membrane lipids. Crystal-packing analysis revealed a previously unseen `dimer-of-dimers' assembly state of N-terminal Wag31, which is formed by antiparallel stacking of two coiled-coil dimers. Size-exclusion column-chromatography-coupled small-angle solution X-ray scattering data revealed a tetrameric form as a major assembly state of N-terminal Wag31 in solution, further supporting the crystal structure. The results suggest that, in addition to lipid binding, the N-terminal Wag31 can participate in self-assembly to form filamentous structures. Plausible models of linear self-assembly and branching of Wag31 filaments consistent with available data are suggested.

scholarly journals Crystal structure of the membrane anchoring domain of mycobacterial Wag31: a dimer-of-dimer suggests how a Wag31 filament might self-assemble

2019 ◽  
Author(s):  
Komal Choukate ◽  
Barnali Chaudhuri
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Membrane Surface ◽  
Point Group ◽  
Coiled Coil ◽  
Size Exclusion ◽  
Group Symmetry ◽  
Scattering Data ◽  
Replacement Method ◽  
Membrane Anchoring

AbstractWag31, or DivIVA, is an essential protein and a drug target in human pathogen Mycobacterium tuberculosis that self-assembles at the negatively curved membrane surface to form a higher-order structural scaffold, maintains rod-shaped cellular morphology, and localizes key cell-wall synthesizing proteins at the pole for exclusive polar growth. We determined the crystal structure of N-terminal membrane anchoring domain of mycobacterial Wag31 at 2.3 Å resolution using molecular replacement method. Crystal packing analysis revealed a previously unseen dimer-of-dimer assembly state of N-terminal Wag31 with C2 point group symmetry, which is formed by antiparallel stacking of two coiled coil dimers. Size-exclusion column chromatography-coupled small angle solution X-ray scattering data showed a tetrameric form as a major assembly state of N-terminal Wag31 in solution, further supporting the crystal structure. Plausible models of linear self-assembling, and branching, of Wag31 filaments consistent with available data are suggested.

scholarly journals The Structure and Function of Modular Escherichia coli O157:H7 Bacteriophage FTBEc1 endolysin, LysT84: Defining a New Endolysin Catalytic Subfamily

2021 ◽  
Author(s):  
Michael Love ◽  
David Coombes ◽  
Salim Ismail ◽  
Craig Billington ◽  
Renwick CJ Dobson
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Antibacterial Agents ◽  
Analytical Ultracentrifugation ◽  
Structural Data ◽  
Scattering Data ◽  
Structural Basis ◽  
Escherichia Coli O157 ◽  
Dynamic Simulations ◽  
Enzymatic Function

Bacteriophage endolysins degrade peptidoglycan and have been identified as antibacterial candidates to combat antimicrobial resistance. Considering the catalytic and structural diversity of endolysins, there is a paucity of structural data to inform how these enzymes work at the molecular level—key data that is needed to realize the potential of endolysin-based antibacterial agents. Here, we determine the atomic structure and define the enzymatic function of Escherichia coli O157:H7 phage FTEBc1 endolysin, LysT84. Bioinformatic analysis reveals that LysT84 is a modular endolysin, which is unusual for Gram-negative endolysins, comprising a peptidoglycan binding domain and an enzymatic domain. The crystal structure of LysT84 (2.99 Å) revealed a mostly α-helical protein with two domains connected by a linker region but packed together. LysT84 was determined to be a monomer in solution using analytical ultracentrifugation. Small-angle X-ray scattering data revealed that LysT84 is a flexible protein but does not have the expected bimodal P(r) function of a multidomain protein, suggesting that the domains of LysT84 pack closely creating a globular protein as seen in the crystal structure. Structural analysis reveals two key glutamate residues positioned on either side of the active site cavity; mutagenesis demonstrating these residues are critical for peptidoglycan degradation. Molecular dynamic simulations suggest that the enzymatically active domain is dynamic, allowing the appropriate positioning of these catalytic residues for hydrolysis of the β(1–4) bond. Overall, our study defines the structural basis for peptidoglycan degradation by LysT84 which supports rational engineering of related endolysins into effective antibacterial agents.

scholarly journals The structure of nerve growth factor in complex with lysophosphatidylinositol

2015 ◽  
Vol 71 (7) ◽  
pp. 906-912 ◽  
Author(s):  
Han-Li Sun ◽  
Tao Jiang
Keyword(s):  
Crystal Structure ◽  
Nerve Growth Factor ◽  
Growth Factor ◽  
Lipid Binding ◽  
Structural Basis ◽  
Recognition Mechanism ◽  
Nerve Growth ◽  
Physiological Processes ◽  
Dimeric Interface ◽  
Specific Lipid

Nerve growth factor (NGF) is an important protein that is involved in a variety of physiological processes in cell survival, differentiation, proliferation and maintenance. The previously reported crystal structure of mouse NGF (mNGF) in complex with lysophosphatidylserine (LysoPS) showed that mNGF can bind LysoPS at its dimeric interface. To expand the understanding of the structural basis for specific lipid recognition by NGF, the crystal structure of mNGF complexed with lysophosphatidylinositol (13:0 LysoPI) was solved. Interestingly, in addition to Lys88, which interacts with the head glycerol group and the phosphate group of LysoPI, as seen in the mNGF–LysoPS structure, two additional residues, Tyr52 and Arg50, were found to assist in lipid binding by forming hydrogen bonds to the inositol moiety of the LysoPI molecule. The results suggest a specific recognition mechanism of inositol group-containing lipids by NGF, which may help in the design of bioactive compounds that can be delivered by NGF.

scholarly journals Structural basis of human 5,10-methylenetetrahydrofolate reductase (MTHFR) regulation by phosphorylation and S-adenosylmethionine inhibition

2018 ◽  
Author(s):  
D. Sean Froese ◽  
Jola Kopec ◽  
Elzbieta Rembeza ◽  
Gustavo Arruda Bezerra ◽  
Anselm Erich Oberholzer ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Methylenetetrahydrofolate Reductase ◽  
Binding Domain ◽  
Structural Basis ◽  
Methyl Donor ◽  
Tim Barrel ◽  
Conformational Plasticity ◽  
Methionine Cycle ◽  
Regulatory Connection

AbstractThe folate and methionine cycles are crucial to the biosynthesis of lipids, nucleotides and proteins, and production of the global methyl donor S-adenosylmethionine (SAM). 5,10-methylenetetrahydrofolate reductase (MTHFR) represents a key regulatory connection between these cycles, generating 5-methyltetrahydrofolate for initiation of the methionine cycle, and undergoing allosteric inhibition by its end product SAM. Our 2.5 Å resolution crystal structure of human MTHFR reveals a unique architecture, appending the well-conserved catalytic TIM-barrel to a eukaryote-only SAM-binding domain. The latter domain of novel fold provides the predominant interface for MTHFR homo-dimerization, positioning the N-terminal serine-rich phosphorylation region into proximity with the C-terminal SAM-binding domain. This explains how MTHFR phosphorylation, identified on 11 N-terminal residues (16-total), increases sensitivity to SAM binding and inhibition. Finally, we demonstrate the 25-amino-acid inter-domain linker enables conformational plasticity and propose it to be a key mediator of SAM regulation.

1-[5-(4,5-Dimethyl-1,3,2-dioxaborolan-2-yl)thiophen-2-yl]ethanone and 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzaldehyde

2012 ◽  
Vol 68 (6) ◽  
pp. o213-o215
Author(s):  
Neudo Urdaneta ◽  
Jesús Nuñez ◽  
Teresa González ◽  
Alexander Briceño
Keyword(s):  
Crystal Structure ◽  
Self Assembly ◽  
Crystal Packing ◽  
Van Der Waals ◽  
Two Dimensional ◽  
Π Interactions ◽  
Methyl Methyl ◽  
Self Organized ◽  
Dipole Interactions ◽  
Dimensional Network

In both title compounds, C10H13BO3S, (I), and C13H17BO3, (II), the molecules adopt nearly planar conformations. The crystal packing of (I) consists of a supramolecular two-dimensional network with a herringbone-like topology formed by self assembly of centrosymmetric pairs of molecules linkedviadipole–dipole interactions. The crystal structure of (II) consists of a supramolecular two-dimensional network built up from centrosymmetric pairs of moleculesviaπ–π interactions. These pairs of molecules are self-organized in an offset fashion related by a symmetry centre, generating supramolecular ribbons running along the [101] direction. Neighbouring ribbons are stackedviacomplementary van der Waals and hydrophobic methyl–methyl interactions.

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