scholarly journals Metal substitution of tetanus neurotoxin

1997 ◽  
Vol 322 (2) ◽  
pp. 507-510 ◽  
Author(s):  
Fiorella TONELLO ◽  
Giampietro SCHIAVO ◽  
Cesare MONTECUCCO
Keyword(s):  
Active Site ◽  
Transition Metal Ions ◽  
Structural Basis ◽  
Metal Substitution ◽  
Absorbance Spectrum ◽  
Independent Family ◽  
Tetanus Neurotoxin ◽  
Highly Active ◽  
Clostridial Neurotoxins ◽  
Definition Of

Tetanus neurotoxin was depleted of its catalytic Zn2+ ion, and the apotoxin was reconstituted with different transition metal ions. The Mn2+- and Co2+-tetanus neurotoxins are highly active in the proteolysis of vesicle-associated membrane protein/synaptobrevin, the natural substrate of this toxin, whereas Cu2+ and Fe2+ minimally supported proteolytic activity. The visible absorbance spectrum of Co2+-tetanus neurotoxin shows a maximum at 538 nm with a molar absorption coefficient of 82 M-1·cm-1. These results indicate that the Zn2+ environment at the active site of tetanus neurotoxin is different from those of known Zn2+-endopeptidases and provide a structural basis for the definition of tetanus neurotoxin, and the related clostridial neurotoxins, as an independent family of metalloproteases.

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.

Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis

2019 ◽  
Vol 476 (6) ◽  
pp. 991-1003 ◽  
Author(s):  
Vijaykumar Pillalamarri ◽  
Tarun Arya ◽  
Neshatul Haque ◽  
Sandeep Chowdary Bala ◽  
Anil Kumar Marapaka ◽  
...  
Keyword(s):  
Natural Product ◽  
Active Site ◽  
Covalent Modification ◽  
Structural Basis ◽  
Wild Type ◽  
Methionine Aminopeptidases ◽  
Synthetic Derivative ◽  
Dynamics Simulations

Abstract Natural product ovalicin and its synthetic derivative TNP-470 have been extensively studied for their antiangiogenic property, and the later reached phase 3 clinical trials. They covalently modify the conserved histidine in Type 2 methionine aminopeptidases (MetAPs) at nanomolar concentrations. Even though a similar mechanism is possible in Type 1 human MetAP, it is inhibited only at millimolar concentration. In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulations suggest that ovalicin is not stably placed in the active site of wild-type MetAP1b before the covalent modification. In the case of F309M mutant and human Type 2 MetAP, molecule spends more time in the active site providing time for covalent modification.

Polytypes and polytypism

1986 ◽  
Vol 176 (3-4) ◽  
Author(s):  
R. J. Angel
Keyword(s):  
Structural Variation ◽  
Structural Basis ◽  
Definition Of ◽  
Alloy Systems

AbstractThe definition of polytypism recommended by the IMA/IUCr joint committee on nomenclature is reviewed in the light of the structural variation observed in mineral and alloy systems. As a result of this review it is concluded that previous definitions of polytypism are too restrictive to be practical, and a definition which emphasises the structural basis of polytypism is proposed:“Polytypism arises from the different modes of stacking of one or more structurally compatible modules.”The various types of structural variation included under this definition are described using as examples minerals, ceramics, and alloys.

scholarly journals Structural basis for an atypical active site of anl-aspartate/glutamate-specific racemase fromEscherichia coli

FEBS Letters ◽  
2015 ◽  
Vol 589 (24PartB) ◽  
pp. 3842-3847 ◽  
Author(s):  
Jae-Woo Ahn ◽  
Jeong Ho Chang ◽  
Kyung-Jin Kim
Keyword(s):  
Active Site ◽  
Structural Basis ◽  
Fromescherichia Coli

scholarly journals A Novel Tetanus Neurotoxin-insensitive Vesicle-associated Membrane Protein in SNARE Complexes of the Apical Plasma Membrane of Epithelial Cells

1998 ◽  
Vol 9 (6) ◽  
pp. 1437-1448 ◽  
Author(s):  
Thierry Galli ◽  
Ahmed Zahraoui ◽  
Vadakkanchery V. Vaidyanathan ◽  
Graça Raposo ◽  
Jian Min Tian ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Epithelial Cells ◽  
Membrane Protein ◽  
Apical Plasma Membrane ◽  
Domain Specific ◽  
Tetanus Neurotoxin ◽  
Synaptic Vesicle Exocytosis ◽  
Clostridial Neurotoxins ◽  
Vesicle Exocytosis ◽  
Syntaxin 3

The importance of soluble N-ethyl maleimide (NEM)-sensitive fusion protein (NSF) attachment protein (SNAP) receptors (SNAREs) in synaptic vesicle exocytosis is well established because it has been demonstrated that clostridial neurotoxins (NTs) proteolyze the vesicle SNAREs (v-SNAREs) vesicle-associated membrane protein (VAMP)/brevins and their partners, the target SNAREs (t-SNAREs) syntaxin 1 and SNAP25. Yet, several exocytotic events, including apical exocytosis in epithelial cells, are insensitive to numerous clostridial NTs, suggesting the presence of SNARE-independent mechanisms of exocytosis. In this study we found that syntaxin 3, SNAP23, and a newly identified VAMP/brevin, tetanus neurotoxin (TeNT)-insensitive VAMP (TI-VAMP), are insensitive to clostridial NTs. In epithelial cells, TI-VAMP–containing vesicles were concentrated in the apical domain, and the protein was detected at the apical plasma membrane by immunogold labeling on ultrathin cryosections. Syntaxin 3 and SNAP23 were codistributed at the apical plasma membrane where they formed NEM-dependent SNARE complexes with TI-VAMP and cellubrevin. We suggest that TI-VAMP, SNAP23, and syntaxin 3 can participate in exocytotic processes at the apical plasma membrane of epithelial cells and, more generally, domain-specific exocytosis in clostridial NT-resistant pathways.

scholarly journals Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii

2018 ◽  
Vol 74 (12) ◽  
pp. 765-769 ◽  
Author(s):  
Tzu-Ping Ko ◽  
Chi-Hung Huang ◽  
Shu-Jung Lai ◽  
Yeh Chen
Keyword(s):  
Acinetobacter Baumannii ◽  
Active Site ◽  
Multidrug Resistant ◽  
Structural Basis ◽  
X Ray Diffraction ◽  
X Ray ◽  
Peptidoglycan Synthesis ◽  
C Terminus ◽  
Dimeric Protein ◽  
Β Sheet

Undecaprenyl pyrophosphate (UPP) is an important carrier of the oligosaccharide component in peptidoglycan synthesis. Inhibition of UPP synthase (UPPS) may be an effective strategy in combating the pathogen Acinetobacter baumannii, which has evolved to be multidrug-resistant. Here, A. baumannii UPPS (AbUPPS) was cloned, expressed, purified and crystallized, and its structure was determined by X-ray diffraction. Each chain of the dimeric protein folds into a central β-sheet with several surrounding α-helices, including one at the C-terminus. In the active site, two molecules of citrate interact with the side chains of the catalytic aspartate and serine. These observations may provide a structural basis for inhibitor design against AbUPPS.

scholarly journals Structural comparisons lead to the definition of a new superfamily of NAD(P)(H)-accepting oxidoreductases: the single-domain reductases/epimerases/dehydrogenases (the ‘RED’ family)

1994 ◽  
Vol 304 (1) ◽  
pp. 95-99 ◽  
Author(s):  
G Labesse ◽  
A Vidal-Cros ◽  
J Chomilier ◽  
M Gaudry ◽  
J P Mornon
Keyword(s):  
Amino Acids ◽  
Sequence Alignment ◽  
Active Site ◽  
Tertiary Structure ◽  
Binding Specificity ◽  
Single Domain ◽  
Divergent Evolution ◽  
Cofactor Binding ◽  
Sequence Identity ◽  
Definition Of

Using both primary- and tertiary-structure comparisons, we have established new structural similarities shared by reductases, epimerases and dehydrogenases not previously known to be related. Despite the low sequence identity (down to 10%), short consensus segments are identified. We show that the sequence, the active site and the supersecondary structure are well conserved in these proteins. New homologues (the protochlorophyllide reductases) are detected, and we define a new superfamily composed of single-domain dinucleotide-binding enzymes. Rules for the cofactor-binding specificity are deduced from our sequence alignment. The involvement of some amino acids in catalysis is discussed. Comparison with two-domain dehydrogenases allows us to distinguish two general mechanisms of divergent evolution.

scholarly journals Stepwise maturation of the peptidyl transferase region of human mitoribosomes

2021 ◽  
Author(s):  
Tea Lenarcic ◽  
Mateusz Jaskolowski ◽  
Marc Leibundgut ◽  
Alain Scaiola ◽  
Tanja Schoenhut ◽  
...  
Keyword(s):  
Quality Control ◽  
16S Rrna ◽  
Active Site ◽  
Critical Role ◽  
Ribosomal Subunit ◽  
Structural Basis ◽  
Ribosome Assembly ◽  
Peptidyl Transferase ◽  
Mitochondrial Ribosomes ◽  
Mitochondrial Ribosome

Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. Structural basis of the mammalian mitochondrial ribosome assembly is currently not understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving 7 assembly factors. We discover that NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by MRM2 methyltransferase and quality control interactions with a conserved mitochondrial GTPase MTG2 that contacts the sarcin ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.

scholarly journals The Architecture and the Pace of the Press-Marathon of the President of Ukraine V. Zelensky

2020 ◽  
pp. 113-120
Author(s):  
Kostyantin Hrubych
Keyword(s):  
Scientific Literature ◽  
Human Perception ◽  
Communication Technologies ◽  
Structural Basis ◽  
The Press ◽  
Food Market ◽  
Empirical Research Methods ◽  
Main Components ◽  
Definition Of ◽  
Structural Base

The main schemes of architectonics, which is a structural base of television action, general outward form of construction and interrelation of its parts, their correlation to each other are determined. The pattern of application of archetypical principle of human perception of stories from Aristotle’s first works to use of communication technologies of proportionality of journalist’s text construction by contemporary TV reporters and screenwriters are researched. The novelty of the study is in an attempt to segregate clearly the notions of script composition from architectonics, the essence of difference of priority of the rhythm category namely for architectonics. The objective of the study is to determine the basic schemes of architectonics which is the structural basis of television action, the general appearance and interrelation of its parts, their correlation with each other. Such empirical research methods as observation, abstraction and analysis have been applied. The result of the study was the analysis of television scripts of various programs, definition of main components of architectonics – its beginning, middle and end parts, as well as presentation of structural diagrams of script architectonics. It is emphasized that the action in the scenario should be organized in such way that the dramatic tension curve and the viewer interest curve are being evenly raised from the beginning to the end of the spectacle. The scenario construction of a record-breaking press-marathon with the President of Ukraine Volodymyr Zelenskyi that took place on October 10, 2019 in the capital of Ukraine at Kyiv Food Market was first studied in the scientific literature.

scholarly journals Structural basis for UFM1 transfer from UBA5 to UFC1

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Manoj Kumar ◽  
Prasanth Padala ◽  
Jamal Fahoum ◽  
Fouad Hassouna ◽  
Tomer Tsaban ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Structural Basis ◽  
Adenylation Domain ◽  
Post Translational Modification ◽  
Target Proteins ◽  
Cellular Processes ◽  
Enzyme Cascade ◽  
Linear Sequence ◽  
C Terminus

AbstractUfmylation is a post-translational modification essential for regulating key cellular processes. A three-enzyme cascade involving E1, E2 and E3 is required for UFM1 attachment to target proteins. How UBA5 (E1) and UFC1 (E2) cooperatively activate and transfer UFM1 is still unclear. Here, we present the crystal structure of UFC1 bound to the C-terminus of UBA5, revealing how UBA5 interacts with UFC1 via a short linear sequence, not observed in other E1-E2 complexes. We find that UBA5 has a region outside the adenylation domain that is dispensable for UFC1 binding but critical for UFM1 transfer. This region moves next to UFC1’s active site Cys and compensates for a missing loop in UFC1, which exists in other E2s and is needed for the transfer. Overall, our findings advance the understanding of UFM1’s conjugation machinery and may serve as a basis for the development of ufmylation inhibitors.

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