Structural basis for non-catalytic and catalytic activities of ribonuclease III

2006 ◽  
Vol 62 (8) ◽  
pp. 933-940 ◽  
Author(s):  
Xinhua Ji
Keyword(s):  
Structural Basis ◽  
Ribonuclease Iii ◽  
Catalytic Activities

scholarly journals Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase

2020 ◽  
Vol 117 (33) ◽  
pp. 19914-19925 ◽  
Author(s):  
Anahita Daruwalla ◽  
Jianye Zhang ◽  
Ho Jun Lee ◽  
Nimesh Khadka ◽  
Erik R. Farquhar ◽  
...  
Keyword(s):  
Active Site ◽  
Molecular Basis ◽  
Structural Basis ◽  
Reaction Intermediates ◽  
Catalytic Activities ◽  
Selective Stabilization ◽  
Carotenoid Cleavage Dioxygenases ◽  
Active Site Cavity ◽  
Binding Cleft ◽  
Shed Light

Apocarotenoids are important signaling molecules generated from carotenoids through the action of carotenoid cleavage dioxygenases (CCDs). These enzymes have a remarkable ability to cleave carotenoids at specific alkene bonds while leaving chemically similar sites within the polyene intact. Although several bacterial and eukaryotic CCDs have been characterized, the long-standing goal of experimentally visualizing a CCD–carotenoid complex at high resolution to explain this exquisite regioselectivity remains unfulfilled. CCD genes are also present in some archaeal genomes, but the encoded enzymes remain uninvestigated. Here, we address this knowledge gap through analysis of a metazoan-like archaeal CCD fromCandidatusNitrosotalea devanaterra (NdCCD).NdCCD was active toward β-apocarotenoids but did not cleave bicyclic carotenoids. It exhibited an unusual regiospecificity, cleaving apocarotenoids solely at the C14′–C13′ alkene bond to produce β-apo-14′-carotenals. The structure ofNdCCD revealed a tapered active site cavity markedly different from the broad active site observed for the retinal-formingSynechocystisapocarotenoid oxygenase (SynACO) but similar to the vertebrate retinoid isomerase RPE65. The structure ofNdCCD in complex with its apocarotenoid product demonstrated that the site of cleavage is defined by interactions along the substrate binding cleft as well as selective stabilization of reaction intermediates at the scissile alkene. These data on the molecular basis of CCD catalysis shed light on the origins of the varied catalytic activities found in metazoan CCDs, opening the possibility of modifying their activity through rational chemical or genetic approaches.

scholarly journals Structural and Functional Studies of 3-Deoxy-D-arabino- Heptulosonate 7-Phosphate Synthase from Prevotella nigrescens

2021 ◽  
Author(s):  
◽  
Yu Bai
Keyword(s):  
Protein Domains ◽  
Chorismate Mutase ◽  
Structural Basis ◽  
Resonance Spectroscopy ◽  
Domain Interaction ◽  
Allosteric Inhibition ◽  
Catalytic Activities ◽  
Prevotella Nigrescens ◽  
Multifunctional Enzymes ◽  
Phosphate Synthase

<p>Multifunctional enzymes, bearing two or more catalytic activities, provide exceptional contributions to the efficient and coherent function of metabolic pathways. Two main benefits of multifunctional enzymes have been clearly described. Firstly, linked catalytic modules can enhance the overall catalytic rate for consecutive reactions of a metabolic pathway due to substrate channelling. Secondly, the fusion of two protein domains can impart allosteric control, such that the catalytic function of one of the protein domains is altered by a ligand binding to the second, covalently linked domain. This study examines a bifunctional enzyme comprising a 3-deoxy-D-arabino heptulosonate 7-phosphate synthase (DAH7PS) domain covalently fused to a C-terminal chorismate mutase (CM) domain from Prevotella nigrescens (PniDAH7PS). DAH7PS catalyses the first reaction of the shikimate pathway leading to the biosynthesis of aromatic amino acids, whereas CM functions at a pathway branch point, leading to the biosynthesis of tyrosine and phenylalanine. Through the investigation of PniDAH7PS, a special functional interdependence between the two non-consecutive catalytic functionalities and the derived allosteric regulation was unravelled.  Chapter 2 generally characterises the biochemical and structural features of PniDAH7PS. The two catalytic activities exhibit substantial hetero-interdependency and the separation of the two distinct catalytic domains results in a dramatic loss of both the DAH7PS and CM enzymatic activities. The structural investigation into this protein revealed a unique dimeric assembly and implicates a hetero-interaction between the DAH7PS and CM domains, providing a structural basis for the functional interdependence. Moreover, allosteric inhibition of DAH7PS by prephenate, the product of the CM-catalysed reaction, was observed. This allostery is accompanied by a striking conformational change, as observed by SAXS, implying that a manipulation of the hetero-domain interaction is the mechanism underpinning the allosteric inhibition.  Chapter 3 looks into the mechanism underpinning the DAH7PS and CM functional interdependence. Rearrangements of the conformation of PniDAH7PS following the addition of substrate combinations were observed. This indicates that a dynamic interaction between the DAH7PS and CM domains is important for catalysis. Furthermore, perturbation of these conformational variations by either a truncation mutation in the CM domain or the presence of a high concentration of NaCl interrupted the both the DAH7PS and CM catalytic activities, implying that a dynamic hetero-domain interaction is essential for the delivering the normal DAH7PS and CM functions. This work also reveals a dual role for the DAH7PS domain, exerting catalysis and allosteric activation on the CM activity simultaneously.  Chapter 4 investigates the mechanism of the allosteric inhibition of PniDAH7PS by prephenate. The structural effect of prephenate on PniDAH7PS, with the addition of substrate combinations, was inspected, and the results unravelled the same conformation of PniDAH7PS under different conditions, exhibiting high compactness and rigidity. This finding indicates that the probable inhibitory effect of prephenate on PniDAH7PS is realised by freezing the enzyme’s structure in order to deprive PniDAH7PS of the dynamic-dependent catalytic activity.  Chapter 5 describes the development of a method for producing segmentally isotopically labelled PniDAH7PS using Expressed Protein Ligation (EPL). This chapter also details attempts to couple this method with small angle neutron scattering (SANS) and nuclear magnetic resonance spectroscopy (NMR) to gain more structural information regarding the catalytic and allosteric properties of PniDAH7PS.</p>

scholarly journals Structural and Functional Studies of 3-Deoxy-D-arabino- Heptulosonate 7-Phosphate Synthase from Prevotella nigrescens

2021 ◽  
Author(s):  
◽  
Yu Bai
Keyword(s):  
Protein Domains ◽  
Chorismate Mutase ◽  
Structural Basis ◽  
Resonance Spectroscopy ◽  
Domain Interaction ◽  
Allosteric Inhibition ◽  
Catalytic Activities ◽  
Prevotella Nigrescens ◽  
Multifunctional Enzymes ◽  
Phosphate Synthase

<p>Multifunctional enzymes, bearing two or more catalytic activities, provide exceptional contributions to the efficient and coherent function of metabolic pathways. Two main benefits of multifunctional enzymes have been clearly described. Firstly, linked catalytic modules can enhance the overall catalytic rate for consecutive reactions of a metabolic pathway due to substrate channelling. Secondly, the fusion of two protein domains can impart allosteric control, such that the catalytic function of one of the protein domains is altered by a ligand binding to the second, covalently linked domain. This study examines a bifunctional enzyme comprising a 3-deoxy-D-arabino heptulosonate 7-phosphate synthase (DAH7PS) domain covalently fused to a C-terminal chorismate mutase (CM) domain from Prevotella nigrescens (PniDAH7PS). DAH7PS catalyses the first reaction of the shikimate pathway leading to the biosynthesis of aromatic amino acids, whereas CM functions at a pathway branch point, leading to the biosynthesis of tyrosine and phenylalanine. Through the investigation of PniDAH7PS, a special functional interdependence between the two non-consecutive catalytic functionalities and the derived allosteric regulation was unravelled.  Chapter 2 generally characterises the biochemical and structural features of PniDAH7PS. The two catalytic activities exhibit substantial hetero-interdependency and the separation of the two distinct catalytic domains results in a dramatic loss of both the DAH7PS and CM enzymatic activities. The structural investigation into this protein revealed a unique dimeric assembly and implicates a hetero-interaction between the DAH7PS and CM domains, providing a structural basis for the functional interdependence. Moreover, allosteric inhibition of DAH7PS by prephenate, the product of the CM-catalysed reaction, was observed. This allostery is accompanied by a striking conformational change, as observed by SAXS, implying that a manipulation of the hetero-domain interaction is the mechanism underpinning the allosteric inhibition.  Chapter 3 looks into the mechanism underpinning the DAH7PS and CM functional interdependence. Rearrangements of the conformation of PniDAH7PS following the addition of substrate combinations were observed. This indicates that a dynamic interaction between the DAH7PS and CM domains is important for catalysis. Furthermore, perturbation of these conformational variations by either a truncation mutation in the CM domain or the presence of a high concentration of NaCl interrupted the both the DAH7PS and CM catalytic activities, implying that a dynamic hetero-domain interaction is essential for the delivering the normal DAH7PS and CM functions. This work also reveals a dual role for the DAH7PS domain, exerting catalysis and allosteric activation on the CM activity simultaneously.  Chapter 4 investigates the mechanism of the allosteric inhibition of PniDAH7PS by prephenate. The structural effect of prephenate on PniDAH7PS, with the addition of substrate combinations, was inspected, and the results unravelled the same conformation of PniDAH7PS under different conditions, exhibiting high compactness and rigidity. This finding indicates that the probable inhibitory effect of prephenate on PniDAH7PS is realised by freezing the enzyme’s structure in order to deprive PniDAH7PS of the dynamic-dependent catalytic activity.  Chapter 5 describes the development of a method for producing segmentally isotopically labelled PniDAH7PS using Expressed Protein Ligation (EPL). This chapter also details attempts to couple this method with small angle neutron scattering (SANS) and nuclear magnetic resonance spectroscopy (NMR) to gain more structural information regarding the catalytic and allosteric properties of PniDAH7PS.</p>

Organization of tight junctions in the choroid plexus epithelium

1978 ◽  
Vol 36 (2) ◽  
pp. 336-337
Author(s):  
B. Van Deurs ◽  
J. K. Koehler
Keyword(s):  
Choroid Plexus ◽  
Present Report ◽  
Freeze Fracture ◽  
Barrier Properties ◽  
Cell Junctions ◽  
Structural Basis ◽  
Apical Surface ◽  
Choroid Plexus Epithelium ◽  
Solid Nitrogen ◽  
Special Composition

The choroid plexus epithelium constitutes a blood-cerebrospinal fluid (CSF) barrier, and is involved in regulation of the special composition of the CSF. The epithelium is provided with an ouabain-sensitive Na/K-pump located at the apical surface, actively pumping ions into the CSF. The choroid plexus epithelium has been described as “leaky” with a low transepithelial resistance, and a passive transepithelial flux following a paracellular route (intercellular spaces and cell junctions) also takes place. The present report describes the structural basis for these “barrier” properties of the choroid plexus epithelium as revealed by freeze fracture.Choroid plexus from the lateral, third and fourth ventricles of rats were used. The tissue was fixed in glutaraldehyde and stored in 30% glycerol. Freezing was performed either in liquid nitrogen-cooled Freon 22, or directly in a mixture of liquid and solid nitrogen prepared in a special vacuum chamber. The latter method was always used, and considered necessary, when preparations of complementary (double) replicas were made.

High resolution spot scan imaging of frozen, hydrated actin bundles with 400kV electrons

1992 ◽  
Vol 50 (1) ◽  
pp. 512-513
Author(s):  
J. Jakana ◽  
M.F. Schmid ◽  
P. Matsudaira ◽  
W. Chiu
Keyword(s):  
High Resolution ◽  
Binding Proteins ◽  
Actin Binding ◽  
Eukaryotic Cells ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Actin Bundle ◽  
Actin Bundles ◽  
3 Dimensional ◽  
Macromolecular Assembly

Actin is a protein found in all eukaryotic cells. In its polymerized form, the cells use it for motility, cytokinesis and for cytoskeletal support. An example of this latter class is the actin bundle in the acrosomal process from the Limulus sperm. The different functions actin performs seem to arise from its interaction with the actin binding proteins. A 3-dimensional structure of this macromolecular assembly is essential to provide a structural basis for understanding this interaction in relationship to its development and functions.

Electron Microscopy and image reconstruction reveal the structural basis for spectrin's elastic properties

1992 ◽  
Vol 50 (1) ◽  
pp. 510-511
Author(s):  
Amy M. McGough ◽  
Robert Josephs
Keyword(s):  
Electron Microscopy ◽  
Elastic Properties ◽  
Conformational Changes ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Membrane Skeleton ◽  
Projection Algorithm ◽  
Structural Basis ◽  
Iterative Approximation ◽  
Membrane Skeletons

The remarkable deformability of the erythrocyte derives in large part from the elastic properties of spectrin, the major component of the membrane skeleton. It is generally accepted that spectrin's elasticity arises from marked conformational changes which include variations in its overall length (1). In this work the structure of spectrin in partially expanded membrane skeletons was studied by electron microscopy to determine the molecular basis for spectrin's elastic properties. Spectrin molecules were analysed with respect to three features: length, conformation, and quaternary structure. The results of these studies lead to a model of how spectrin mediates the elastic deformation of the erythrocyte.Membrane skeletons were isolated from erythrocyte membrane ghosts, negatively stained, and examined by transmission electron microscopy (2). Particle lengths and end-to-end distances were measured from enlarged prints using the computer program MACMEASURE. Spectrin conformation (straightness) was assessed by calculating the particles’ correlation length by iterative approximation (3). Digitised spectrin images were correlation averaged or Fourier filtered to improve their signal-to-noise ratios. Three-dimensional reconstructions were performed using a suite of programs which were based on the filtered back-projection algorithm and executed on a cluster of Microvax 3200 workstations (4).

Electron diffraction detection of ordliking in annealed PbTe thin film

1990 ◽  
Vol 48 (4) ◽  
pp. 1018-1019
Author(s):  
Karimat El-Sayed
Keyword(s):  
Thin Film ◽  
Electron Diffraction ◽  
Lead Telluride ◽  
Structural Basis ◽  
Face Centered Cubic ◽  
X Ray ◽  
Polycrystalline Thin Films ◽  
Stage Process ◽  
Diffraction Patterns ◽  
Face Centered

Lead telluride is an important semiconductor of many applications. Many Investigators showed that there are anamolous descripancies in most of the electrophysical properties of PbTe polycrystalline thin films on annealing. X-Ray and electron diffraction studies are being undertaken in the present work in order to explain the cause of this anamolous behaviour.Figures 1-3 show the electron diffraction of the unheated, heated in air at 100°C and heated in air at 250°C respectively of a 300°A polycrystalline PbTe thin film. It can be seen that Fig. 1 is a typical [100] projection of a face centered cubic with unmixed (hkl) indices. Fig. 2 shows the appearance of faint superlattice reflections having mixed (hkl) indices. Fig. 3 shows the disappearance of thf superlattice reflections and the appearance of polycrystalline PbO phase superimposed on the [l00] PbTe diffraction patterns. The mechanism of this three stage process can be explained on structural basis as follows :

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

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