Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1

2020 ◽  
Vol 76 (10) ◽  
pp. 982-992
Author(s):  
Prateek Raj ◽  
S. Karthik ◽  
S. M. Arif ◽  
U. Varshney ◽  
M. Vijayan
Keyword(s):  
Intermolecular Interactions ◽  
Mycobacterium Smegmatis ◽  
Structural Data ◽  
Dominant Mode ◽  
Structural Basis ◽  
Nudix Hydrolase ◽  
Diadenosine Polyphosphates ◽  
Enzyme Action ◽  
Molecular Plasticity ◽  
Ligand Conformation

Mycobacterium smegmatis MutT1 (MsMutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of MsMutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes MsMutT1 a versatile enzyme.

scholarly journals Structural insights into the conformational plasticity of the full-length trimeric HIV-1 envelope glycoprotein precursor

2018 ◽  
Author(s):  
Shijian Zhang ◽  
Wei Li Wang ◽  
Shuobing Chen ◽  
Maolin Lu ◽  
Eden P. Go ◽  
...  
Keyword(s):  
Viral Entry ◽  
Envelope Glycoprotein ◽  
Structural Data ◽  
Full Length ◽  
Heptad Repeat ◽  
Structural Basis ◽  
Glycoprotein Precursor ◽  
Helix Bundle ◽  
Conformational Plasticity ◽  
Hiv 1

SummaryThe human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer mediates viral entry into cells and is the major target for the host antibody response. In infected cells, the mature Env [(gp120/gp41)3] is produced by cleavage of a trimeric gp160 precursor. Proteolytic cleavage decreases Env conformational flexibility, allowing the mature Env to resist antibody binding to conserved elements. The conformational plasticity of the Env precursor skews the humoral immune response towards the elicitation of ineffectual antibodies, contributing to HIV-1 persistence in the infected host. The structural basis for the plasticity of the Env precursor remains elusive. Here we use cryo-electron microscopy to visualize two coexisting conformational states of the full-length Env precursor at nominal resolutions of 5.5 and 8.0 Å. The State-P2 conformation features a three-helix bundle of the gp41 heptad repeat region in the core, but has disordered membrane-interactive regions. State-P1 trimers lack the three-helix bundle and instead retain ordered transmembrane and membrane-proximal external regions embracing a central cavity. Our structural data shed light on the unusual plasticity of the Env precursor and provide new clues to Env immunogen discovery.

scholarly journals Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria

2020 ◽  
Vol 117 (28) ◽  
pp. 16324-16332
Author(s):  
Xiaobo Chen ◽  
Jiayue Chen ◽  
Bing Yan ◽  
Wei Zhang ◽  
Luke W. Guddat ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Mycobacterium Smegmatis ◽  
Hydrophobic Interactions ◽  
Carbon Chain ◽  
Structural Basis ◽  
Broad Substrate Specificity ◽  
Carbon Chains ◽  
Binding Cavity ◽  
Π Stacking Interaction ◽  
Acyl Coa Dehydrogenases

FadE, an acyl-CoA dehydrogenase, introduces unsaturation to carbon chains in lipid metabolism pathways. Here, we report that FadE5 fromMycobacterium tuberculosis(MtbFadE5) andMycobacterium smegmatis(MsFadE5) play roles in drug resistance and exhibit broad specificity for linear acyl-CoA substrates but have a preference for those with long carbon chains. Here, the structures ofMsFadE5 andMtbFadE5, in the presence and absence of substrates, have been determined. These reveal the molecular basis for the broad substrate specificity of these enzymes. FadE5 interacts with the CoA region of the substrate through a large number of hydrogen bonds and an unusual π–π stacking interaction, allowing these enzymes to accept both short- and long-chain substrates. Residues in the substrate binding cavity reorient their side chains to accommodate substrates of various lengths. Longer carbon-chain substrates make more numerous hydrophobic interactions with the enzyme compared with the shorter-chain substrates, resulting in a preference for this type of substrate.

scholarly journals How Na+ activates thrombin – a review of the functional and structural data

2008 ◽  
Vol 389 (8) ◽  
Author(s):  
James A. Huntington
Keyword(s):  
Crystal Structures ◽  
Blood Coagulation ◽  
Protein C ◽  
Coagulation Factor ◽  
Structural Data ◽  
Monovalent Cation ◽  
Coagulation Cascade ◽  
Structural Basis ◽  
Thrombin Activity ◽  
Great Relevance

Abstract Thrombin is the ultimate coagulation factor; it is the final protease generated in the blood coagulation cascade and is the effector of clot formation. Regulation of thrombin activity is thus of great relevance to determining the correct haemostatic balance, with dysregulation leading to bleeding or thrombosis. One of the most enigmatic and controversial regulators of thrombin activity is the monovalent cation Na+. When bound to Na+, thrombin adopts a ‘fast’ conformation which cleaves all procoagulant substrates more rapidly, and when free of Na+, thrombin reverts to a ‘slow’ state which preferentially activates the protein C anticoagulant pathway. Thus, Na+-binding allosterically modulates the activity of thrombin and helps determine the haemostatic balance. Over the last 30 years, there has been much research investigating the structural basis of thrombin allostery. Biochemical and mutagenesis studies established which regions and residues are involved in the slow→fast conformational change, and recently several crystal structures of the putative slow form have been solved. In this article, the biochemical and crystallographic data are reviewed to see if we are any closer to understanding the conformational basis of the Na+ activation of thrombin.

scholarly journals Structural basis for small molecule targeting of Doublecortin Like Kinase 1 DCLK1

2021 ◽  
Author(s):  
Onisha Patel ◽  
Michael Roy ◽  
Ashleigh Kropp ◽  
Weiwen Dai ◽  
Isabelle Lucet
Keyword(s):  
Kinase Inhibitor ◽  
Critical Role ◽  
Structural Data ◽  
Kinase Domain ◽  
Microtubule Assembly ◽  
Systematic Evaluation ◽  
Structural Basis ◽  
Allosteric Site ◽  
Functional Protein ◽  
Wide Range

Abstract Doublecortin-like kinase 1 (DCLK1) is a bi-functional protein classified as a Microtubule-Associated Protein (MAP) and as a serine/threonine kinase that plays a critical role in regulating microtubule assembly. This understudied kinase is upregulated or mutated in a wide range of cancers. Knockdown studies have shown that DCLK1 is functionally important for tumour growth. However, the presence of tissue and development specific spliced DCLK1 isoforms and the lack of systematic evaluation of their biological function have challenged the development of effective strategies to understand the role of DCLK1 in oncogenesis. Recently, DCLK1-IN-1 was reported as a potent and selective DCLK1 kinase inhibitor, a powerful new tool to dissect DCLK1 biological functions. Here, we report the crystal structures of DCLK1 kinase domain in complex with two DCLK1-IN-1 precursors and DCLK-IN-1. Combined, our structural data analysis illuminates and rationalises the structure-activity relationship that informed development of DCLK1-IN-1 and provides the basis for DCLK1-IN-1 increased selectivity. We show that DCLK1-IN-1 induces a drastic conformational change of the N-lobe, which uncovered a new allosteric site. In addition, we demonstrate that DCLK1-IN-1 binds DCLK1 long isoforms with high affinity but does not prevent DCLK1 MAP function. Together, our work outlines the need for in-depth studies to rationally design of isoform-specific modulators and provides an invaluable structural platform to further the design of selective DCLK1 therapeutic agents.

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 Structural basis for antibody binding to adenylate cyclase toxin reveals RTX linkers as neutralization-sensitive epitopes

2021 ◽  
Vol 17 (9) ◽  
pp. e1009920
Author(s):  
Jory A. Goldsmith ◽  
Andrea M. DiVenere ◽  
Jennifer A. Maynard ◽  
Jason S. McLellan
Keyword(s):  
Adenylate Cyclase ◽  
Neutralizing Antibodies ◽  
Neutralizing Antibody ◽  
Structural Data ◽  
Antibody Binding ◽  
Structural Basis ◽  
Antibody Titers ◽  
Adenylate Cyclase Toxin ◽  
Blocking Antibodies

RTX leukotoxins are a diverse family of prokaryotic virulence factors that are secreted by the type 1 secretion system (T1SS) and target leukocytes to subvert host defenses. T1SS substrates all contain a C-terminal RTX domain that mediates recruitment to the T1SS and drives secretion via a Brownian ratchet mechanism. Neutralizing antibodies against the Bordetella pertussis adenylate cyclase toxin, an RTX leukotoxin essential for B. pertussis colonization, have been shown to target the RTX domain and prevent binding to the αMβ2 integrin receptor. Knowledge of the mechanisms by which antibodies bind and neutralize RTX leukotoxins is required to inform structure-based design of bacterial vaccines, however, no structural data are available for antibody binding to any T1SS substrate. Here, we determine the crystal structure of an engineered RTX domain fragment containing the αMβ2-binding site bound to two neutralizing antibodies. Notably, the receptor-blocking antibodies bind to the linker regions of RTX blocks I–III, suggesting they are key neutralization-sensitive sites within the RTX domain and are likely involved in binding the αMβ2 receptor. As the engineered RTX fragment contained these key epitopes, we assessed its immunogenicity in mice and showed that it elicits similar neutralizing antibody titers to the full RTX domain. The results from these studies will support the development of bacterial vaccines targeting RTX leukotoxins, as well as next-generation B. pertussis vaccines.

scholarly journals Investigations of the Contribution of a Putative Glycine Hinge to Ryanodine Receptor Channel Gating

2013 ◽  
Vol 288 (23) ◽  
pp. 16671-16679 ◽  
Author(s):  
Joanne Euden ◽  
Sammy A. Mason ◽  
Cedric Viero ◽  
N. Lowri Thomas ◽  
Alan J. Williams
Keyword(s):  
Ryanodine Receptor ◽  
Striated Muscle ◽  
Transmembrane Helix ◽  
Channel Gating ◽  
Disease Process ◽  
Structural Data ◽  
Structural Basis ◽  
Detailed Knowledge ◽  
Ion Translocation ◽  
Channel Opening

Ryanodine receptor channels (RyR) are key components of striated muscle excitation-contraction coupling, and alterations in their function underlie both inherited and acquired disease. A full understanding of the disease process will require a detailed knowledge of the mechanisms and structures involved in RyR function. Unfortunately, high-resolution structural data, such as exist for K+-selective channels, are not available for RyR. In the absence of these data, we have used modeling to identify similarities in the structural elements of K+ channel pore-forming regions and postulated equivalent regions of RyR. This has identified a sequence of residues in the cytosolic cavity-lining transmembrane helix of RyR (G4864LIIDA4869 in RyR2) analogous to the glycine hinge motif present in many K+ channels. Gating in these K+ channels can be disrupted by substitution of residues for the hinge glycine. We investigated the involvement of glycine 4864 in RyR2 gating by monitoring properties of recombinant human RyR2 channels in which this glycine is replaced by residues that alter gating in K+ channels. Our data demonstrate that introducing alanine at position 4864 produces no significant change in RyR2 function. In contrast, function is altered when glycine 4864 is replaced by either valine or proline, the former preventing channel opening and the latter modifying both ion translocation and gating. Our studies reveal novel information on the structural basis of RyR gating, identifying both similarities with, and differences from, K+ channels. Glycine 4864 is not absolutely required for channel gating, but some flexibility at this point in the cavity-lining transmembrane helix is necessary for normal RyR function.

scholarly journals Crystallization and preliminary X-ray characterization of MutT2, MSMEG_5148 fromMycobacterium smegmatis

2014 ◽  
Vol 70 (2) ◽  
pp. 190-192 ◽  
Author(s):  
S. M. Arif ◽  
P. B. Sang ◽  
U. Varshney ◽  
M. Vijayan
Keyword(s):  
Mycobacterium Smegmatis ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
Nudix Hydrolase ◽  
X Ray Diffraction ◽  
Orthorhombic Unit Cell ◽  
X Ray

Crystallization of MutT2, MSMEG_5148 fromMycobacterium smegmatis, has been carried out and the crystals have been characterized using X-ray diffraction. Matthews coefficient calculation suggests the possibility of one protein molecule in the asymmetric unit of the orthorhombic unit cell, space groupP21212 orP2122. Solution of the structure of the protein by molecular replacement using the known three-dimensional structure of a bacterial Nudix hydrolase is envisaged.

scholarly journals Structural basis for distinctive recognition of fibrinogen γC peptide by the platelet integrin αIIbβ3

2008 ◽  
Vol 182 (4) ◽  
pp. 791-800 ◽  
Author(s):  
Timothy A. Springer ◽  
Jianghai Zhu ◽  
Tsan Xiao
Keyword(s):  
Metal Ion ◽  
Structural Data ◽  
Structural Basis ◽  
Side Chain ◽  
Α Subunit ◽  
Integrin Αiibβ3 ◽  
Rgd Motif ◽  
Γ Subunit ◽  
Fibrinogen Binding ◽  
C Terminus

Hemostasis and thrombosis (blood clotting) involve fibrinogen binding to integrin αIIbβ3 on platelets, resulting in platelet aggregation. αvβ3 binds fibrinogen via an Arg-Asp-Gly (RGD) motif in fibrinogen's α subunit. αIIbβ3 also binds to fibrinogen; however, it does so via an unstructured RGD-lacking C-terminal region of the γ subunit (γC peptide). These distinct modes of fibrinogen binding enable αIIbβ3 and αvβ3 to function cooperatively in hemostasis. In this study, crystal structures reveal the integrin αIIbβ3–γC peptide interface, and, for comparison, integrin αIIbβ3 bound to a lamprey γC primordial RGD motif. Compared with RGD, the GAKQAGDV motif in γC adopts a different backbone configuration and binds over a more extended region. The integrin metal ion–dependent adhesion site (MIDAS) Mg2+ ion binds the γC Asp side chain. The adjacent to MIDAS (ADMIDAS) Ca2+ ion binds the γC C terminus, revealing a contribution for ADMIDAS in ligand binding. Structural data from this natively disordered γC peptide enhances our understanding of the involvement of γC peptide and integrin αIIbβ3 in hemostasis and thrombosis.

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