scholarly journals The endo-β-agarases AgaA and AgaB from the marine bacterium Zobellia galactanivorans: two paralogue enzymes with different molecular organizations and catalytic behaviours

2005 ◽  
Vol 385 (3) ◽  
pp. 703-713 ◽  
Author(s):  
Murielle JAM ◽  
Didier FLAMENT ◽  
Julie ALLOUCH ◽  
Philippe POTIN ◽  
Laurent THION ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Catalytic Domain ◽  
Solid Phase ◽  
Gel Filtration ◽  
Modular Architecture ◽  
Catalytic Domains ◽  
Anomeric Configuration ◽  
Catalytic Module ◽  
Pseudoalteromonas Atlantica ◽  
Random Manner

Two β-agarase genes, agaA and agaB, were functionally cloned from the marine bacterium Zobellia galactanivorans. The agaA and agaB genes encode proteins of 539 and 353 amino acids respectively, with theoretical masses of 60 and 40 kDa. These two β-agarases feature homologous catalytic domains belonging to family GH-16. However, AgaA displays a modular architecture, consisting of the catalytic domain (AgaAc) and two C-terminal domains of unknown function which are processed during secretion of the enzyme. In contrast, AgaB is composed of the catalytic module and a signal peptide similar to the N-terminal signature of prokaryotic lipoproteins, suggesting that this protein is anchored in the cytoplasmic membrane. Gel filtration and electrospray MS experiments demonstrate that AgaB is a dimer in solution, while AgaAc is a monomeric protein. AgaAc and AgaB were overexpressed in Escherichia coli and purified to homogeneity. Both enzymes cleave the β-(1→4) linkages of agarose in a random manner and with retention of the anomeric configuration. Although they behave similarly towards liquid agarose, AgaAc is more efficient than AgaB in the degradation of agarose gels. Given these organizational and catalytic differences, we propose that, reminiscent of the agarolytic system of Pseudoalteromonas atlantica, AgaA is specialized in the initial attack on solid-phase agarose, while AgaB is involved with the degradation of agarose fragments.

Synthesis of hepatitis B surface antigen pre-S2 region fragments and studies on their immunogenicity

1988 ◽  
Vol 53 (11) ◽  
pp. 2952-2956 ◽  
Author(s):  
Bernard Lammek ◽  
Zbigniew Maćkiewicz ◽  
Izabela Derdowska ◽  
Hanna Świderska ◽  
Adam Nowosławski ◽  
...  
Keyword(s):  
Hepatitis B ◽  
Surface Antigen ◽  
Solid Phase ◽  
Hepatitis B Surface Antigen ◽  
Gel Filtration ◽  
Exchange Chromatography ◽  
Antigenic Determinants ◽  
Phase Method ◽  
Peptide Fragments ◽  
Humoral Immune

Two peptide fragments of hepatitis B surface antigen pre-S2 region were synthesized by the solid phase method. The peptides were purified by gel filtration or ion-exchange chromatography on Sephadex SP-C-25. Both peptides induced a cellular and humoral immune response in rabbits. The results showed that fragment 14-22 of pre-S2 region contains one of the antigenic determinants.

scholarly journals Cryo-EM structural analysis of FADD:Caspase-8 complexes defines the catalytic dimer architecture for co-ordinated control of cell fate

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Joanna L. Fox ◽  
Michelle A. Hughes ◽  
Xin Meng ◽  
Nikola A. Sarnowska ◽  
Ian R. Powley ◽  
...  
Keyword(s):  
Cell Death ◽  
Structural Analysis ◽  
Cell Fate ◽  
Catalytic Domain ◽  
Caspase 8 ◽  
Type I ◽  
Signaling Complex ◽  
Catalytic Domains ◽  
Regulated Cell Death ◽  
Death Effector

AbstractRegulated cell death is essential in development and cellular homeostasis. Multi-protein platforms, including the Death-Inducing Signaling Complex (DISC), co-ordinate cell fate via a core FADD:Caspase-8 complex and its regulatory partners, such as the cell death inhibitor c-FLIP. Here, using electron microscopy, we visualize full-length procaspase-8 in complex with FADD. Our structural analysis now reveals how the FADD-nucleated tandem death effector domain (tDED) helical filament is required to orientate the procaspase-8 catalytic domains, enabling their activation via anti-parallel dimerization. Strikingly, recruitment of c-FLIPS into this complex inhibits Caspase-8 activity by altering tDED triple helix architecture, resulting in steric hindrance of the canonical tDED Type I binding site. This prevents both Caspase-8 catalytic domain assembly and tDED helical filament elongation. Our findings reveal how the plasticity, composition and architecture of the core FADD:Caspase-8 complex critically defines life/death decisions not only via the DISC, but across multiple key signaling platforms including TNF complex II, the ripoptosome, and RIPK1/RIPK3 necrosome.

scholarly journals Activity of the Ste20-like kinase, SLK, is enhanced by homodimerization

2011 ◽  
Vol 301 (3) ◽  
pp. F554-F564 ◽  
Author(s):  
Sierra Delarosa ◽  
Julie Guillemette ◽  
Joan Papillon ◽  
Ying-Shan Han ◽  
Arnold S. Kristof ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Gel Filtration ◽  
Coiled Coil ◽  
Kinase Domain ◽  
Kinase Assay ◽  
Luciferase Reporter ◽  
Fk506 Binding Protein ◽  
Induced Apoptosis ◽  
Injury And Repair

The expression and activation of the Ste20-like kinase, SLK, is increased during renal development and recovery from ischemic acute renal failure. SLK promotes apoptosis, and during renal injury and repair, transcriptional induction or posttranscriptional control of SLK may, therefore, regulate cell survival. SLK contains protein interaction (coiled-coil) domains, suggesting that posttranslational homodimerization may also modulate SLK activity. We therefore expressed coiled-coil regions in the C-terminal domain of SLK as fusion proteins and demonstrated their homodimerization. By gel-filtration chromatography, endogenous and heterologously expressed SLK were detected in a macromolecular protein complex. To test the role of homodimerization in kinase activation, we constructed a fusion protein consisting of the SLK catalytic domain (amino acids 1–373) and a modified FK506 binding protein, Fv (Fv-SLK 1–373). Addition of AP20187 (an analog of FK506) enhanced the homodimerization of Fv-SLK 1–373. In an in vitro kinase assay, the dimeric Fv-SLK 1–373 displayed greater kinase activity than the monomeric form. In cells expressing Fv-SLK 1–373, homodimerization increased activation-specific phosphorylation of the proapoptotic kinases, c-Jun N-terminal kinase and p38 kinase. Compared with the monomer, dimeric Fv-SLK 1–373 enhanced the activation of a Bax promoter-luciferase reporter. Finally, expression of Fv-SLK 1–373 induced apoptosis, and the effect was increased by homodimerization. Thus the activity, downstream signaling, and functional effects of SLK are enhanced by dimerization of the kinase domain.

scholarly journals The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain

2014 ◽  
Vol 70 (8) ◽  
pp. 1022-1026 ◽  
Author(s):  
Francois-Xavier Chauviac ◽  
Giles Robertson ◽  
Doris H. X. Quay ◽  
Claire Bagnéris ◽  
Christian Dumas ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Catalytic Domain ◽  
Anomalous Scattering ◽  
Molecular Replacement ◽  
Catalytic Domains ◽  
Domain Composition ◽  
Resuscitation Promoting Factors ◽  
Structural Conservation ◽  
High Degree ◽  
Very High

The first structure of the catalytic domain of RpfC (Rv1884), one of the resuscitation-promoting factors (RPFs) fromMycobacterium tuberculosis, is reported. The structure was solved using molecular replacement once the space group had been correctly identified as twinnedP21rather than the apparentC2221by searching for anomalous scattering sites inP1. The structure displays a very high degree of structural conservation with the previously published structures of the catalytic domains of RpfB (Rv1009) and RpfE (Rv2450). This structural conservation highlights the importance of the versatile domain composition of the RPF family.

scholarly journals Engineered Lysins With Customized Lytic Activities Against Enterococci and Staphylococci

2020 ◽  
Vol 11 ◽  
Author(s):  
Hana Sakina Binte Muhammad Jai ◽  
Linh Chi Dam ◽  
Lowella Servito Tay ◽  
Jodi Jia Wei Koh ◽  
Hooi Linn Loo ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Catalytic Domain ◽  
Therapeutic Potential ◽  
Multidrug Resistant ◽  
Species Specificity ◽  
Resistant Bacteria ◽  
Modular Architecture ◽  
Narrow Spectrum ◽  
Cell Wall Binding ◽  
Peptidoglycan Hydrolysis

The emergence of multidrug-resistant bacteria has made minor bacterial infections incurable with many existing antibiotics. Lysins are phage-encoded peptidoglycan hydrolases that have demonstrated therapeutic potential as a novel class of antimicrobials. The modular architecture of lysins enables the functional domains – catalytic domain (CD) and cell wall binding domain (CBD) – to be shuffled to create novel lysins. The CD is classically thought to be only involved in peptidoglycan hydrolysis whereas the CBD dictates the lytic spectrum of a lysin. While there are many studies that extended the lytic spectrum of a lysin by domain swapping, few have managed to introduce species specificity in a chimeric lysin. In this work, we constructed two chimeric lysins by swapping the CBDs of two parent lysins with different lytic spectra against enterococci and staphylococci. We showed that these chimeric lysins exhibited customized lytic spectra distinct from the parent lysins. Notably, the chimeric lysin P10N-V12C, which comprises a narrow-spectrum CD fused with a broad-spectrum CBD, displayed species specificity not lysing Enterococcus faecium while targeting Enterococcus faecalis and staphylococci. Such species specificity can be attributed to the narrow-spectrum CD of the chimeric lysin. Using flow cytometry and confocal microscopy, we found that the E. faecium cells that were treated with P10N-V12C are less viable with compromised membranes yet remained morphologically intact. Our results suggest that while the CBD is a major determinant of the lytic spectrum of a lysin, the CD is also responsible in the composition of the final lytic spectrum, especially when it pertains to species-specificity.

scholarly journals Identification and characterization of DdPDE3, a cGMP-selective phosphodiesterase from Dictyostelium

2001 ◽  
Vol 353 (3) ◽  
pp. 635-644 ◽  
Author(s):  
Hidekazu KUWAYAMA ◽  
Helena SNIPPE ◽  
Mari DERKS ◽  
Jeroen ROELOFS ◽  
Peter J. M. VAN HAASTERT
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Catalytic Domain ◽  
Expressed Sequence Tag ◽  
Sequence Similarity ◽  
Second Messengers ◽  
Kinetic Properties ◽  
Intracellular Camp ◽  
Catalytic Domains ◽  
Dual Specificity

In Dictyostelium cAMP and cGMP have important functions as first and second messengers in chemotaxis and development. Two cyclic-nucleotide phosphodiesterases (DdPDE 1 and 2) have been identified previously, an extracellular dual-specificity enzyme and an intracellular cAMP-specific enzyme (encoded by the psdA and regA genes respectively). Biochemical data suggest the presence of at least one cGMP-specific phosphodiesterase (PDE) that is activated by cGMP. Using bioinformatics we identified a partial sequence in the Dictyostelium expressed sequence tag database that shows a high degree of amino acid sequence identity with mammalian PDE catalytic domains (DdPDE3). The deduced amino acid sequence of a full-length DdPDE3 cDNA isolated in this study predicts a 60kDa protein with a 300-residue C-terminal PDE catalytic domain, which is preceded by approx. 200 residues rich in asparagine and glutamine residues. Expression of the DdPDE3 catalytic domain in Escherichia coli shows that the enzyme has Michaelis–Menten kinetics and a higher affinity for cGMP (Km = 0.22µM) than for cAMP (Km = 145µM); cGMP does not stimulate enzyme activity. The enzyme requires bivalent cations for activity; Mn2+ is preferred to Mg2+, whereas Ca2+ yields no activity. DdPDE3 is inhibited by 3-isobutyl-1-methylxanthine with an IC50 of approx. 60µM. Overexpression of the DdPDE3 catalytic domain in Dictyostelium confirms these kinetic properties without indications of its activation by cGMP. The properties of DdPDE3 resemble those of mammalian PDE9, which also shows the highest sequence similarity within the catalytic domains. DdPDE3 is the first cGMP-selective PDE identified in lower eukaryotes.

scholarly journals Binding of Ferric Enterobactin by theEscherichia coli Periplasmic Protein FepB

2000 ◽  
Vol 182 (19) ◽  
pp. 5359-5364 ◽  
Author(s):  
Cathy Sprencel ◽  
Zhenghua Cao ◽  
Zengbiao Qi ◽  
Daniel C. Scott ◽  
Marjorie A. Montague ◽  
...  
Keyword(s):  
Specific Activity ◽  
Solid Phase ◽  
Cell Envelope ◽  
Binding Protein ◽  
Gel Filtration ◽  
Periplasmic Protein ◽  
Left Handed ◽  
Fluorescence Measurements ◽  
Rate Limiting Step

ABSTRACT The periplasmic protein FepB of Escherichia coli is a component of the ferric enterobactin transport system. We overexpressed and purified the binding protein 23-fold from periplasmic extracts by ammonium sulfate precipitation and chromatographic methods, with a yield of 20%, to a final specific activity of 15,500 pmol of ferric enterobactin bound/mg. Periplasmic fluid from cells overexpressing the binding protein adsorbed catecholate ferric siderophores with high affinity: in a gel filtration chromatography assay the Kd of the ferric enterobactin-FepB binding reaction was approximately 135 nM. Intrinsic fluorescence measurements of binding by the purified protein, which were more accurate, showed higher affinity for both ferric enterobactin (Kd = 30 nM) and ferric enantioenterobactin (Kd = 15 nM), the left-handed stereoisomer of the natural E. coli siderophore. Purified FepB also adsorbed the apo-siderophore, enterobactin, with comparable affinity (Kd = 60 nM) but did not bind ferric agrobactin. Polyclonal rabbit antisera and mouse monoclonal antibodies raised against nearly homogeneous preparations of FepB specifically recognized it in solid-phase immunoassays. These sera enabled the measurement of the FepB concentration in vivo when expressed from the chromosome (4,000 copies/cell) or from multicopy plasmids (>100,000 copies/cell). Overexpression of the binding protein did not enhance the overall affinity or rate of ferric enterobactin transport, supporting the conclusion that the rate-limiting step of ferric siderophore uptake through the cell envelope is passage through the outer membrane.

scholarly journals The modular architecture of Cellvibrio japonicus mannanases in glycoside hydrolase families 5 and 26 points to differences in their role in mannan degradation

2003 ◽  
Vol 371 (3) ◽  
pp. 1027-1043 ◽  
Author(s):  
Deborah HOGG ◽  
Gavin PELL ◽  
Paul DUPREE ◽  
Florence GOUBET ◽  
Susana M. MARTÍN-ORÚE ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Plant Cell Wall ◽  
Catalytic Domain ◽  
Glycoside Hydrolases ◽  
Crystalline Cellulose ◽  
Carbohydrate Binding ◽  
Molecular Architecture ◽  
Catalytic Domains ◽  
Carbohydrate Binding Modules ◽  
Cellvibrio Japonicus

β-1,4-Mannanases (mannanases), which hydrolyse mannans and glucomannans, are located in glycoside hydrolase families (GHs) 5 and 26. To investigate whether there are fundamental differences in the molecular architecture and biochemical properties of GH5 and GH26 mannanases, four genes encoding these enzymes were isolated from Cellvibrio japonicus and the encoded glycoside hydrolases were characterized. The four genes, man5A, man5B, man5C and man26B, encode the mannanases Man5A, Man5B, Man5C and Man26B, respectively. Man26B consists of an N-terminal signal peptide linked via an extended serine-rich region to a GH26 catalytic domain. Man5A, Man5B and Man5C contain GH5 catalytic domains and non-catalytic carbohydrate-binding modules (CBMs) belonging to families 2a, 5 and 10; Man5C in addition contains a module defined as X4 of unknown function. The family 10 and 2a CBMs bound to crystalline cellulose and ivory nut crystalline mannan, displaying very similar properties to the corresponding family 10 and 2a CBMs from Cellvibrio cellulases and xylanases. CBM5 bound weakly to these crystalline polysaccharides. The catalytic domains of Man5A, Man5B and Man26B hydrolysed galactomannan and glucomannan, but displayed no activity against crystalline mannan or cellulosic substrates. Although Man5C was less active against glucomannan and galactomannan than the other mannanases, it did attack crystalline ivory nut mannan. All the enzymes exhibited classic endo-activity producing a mixture of oligosaccharides during the initial phase of the reaction, although their mode of action against manno-oligosaccharides and glucomannan indicated differences in the topology of the respective substrate-binding sites. This report points to a different role for GH5 and GH26 mannanases from C. japonicus. We propose that as the GH5 enzymes contain CBMs that bind crystalline polysaccharides, these enzymes are likely to target mannans that are integral to the plant cell wall, while GH26 mannanases, which lack CBMs and rapidly release mannose from polysaccharides and oligosaccharides, target the storage polysaccharide galactomannan and manno-oligosaccharides.

scholarly journals Influence of the peptide-chain length on disulphide-bond formation in neurohypophysial hormones and analogues

1978 ◽  
Vol 173 (2) ◽  
pp. 403-409 ◽  
Author(s):  
G Moore
Keyword(s):  
Acetic Acid ◽  
Arginine Vasopressin ◽  
Solid Phase ◽  
Bond Formation ◽  
Gel Filtration ◽  
Arginine Vasotocin ◽  
Disulphide Bond ◽  
Peptide Chain ◽  
Phase Method ◽  
Disulphide Bond Formation

(8-Arginine)vasopressin, (8-arginine)vasotocin, oxytocin and oxypressin, the ‘ring’ derivatives pressinamide and tocinamide, and the extended-chain analogues Pro-Arg-Val-(8-arginine)vasopressin and (8-arginine)vasopressinoyl-Ala-Met-Ala-NH(2), were synthesized by the solid-phase method and purified by sequential gel filtration on Sephadex G-15 in 50% acetic acid and 0.2M-acetic acid. Controlled oxidation of the thiol groups of the reduced peptides obtained after deprotection with sodium in liquid ammonia gave rise to products that depended on the length of the peptide chain: (i) nonapeptides gave monomer and dimer species, (ii) hexapeptides produced mixtures containing higher polymers, and (iii) dodecapeptides gave predominantly monomer with some dimerized material. The evidence suggests that the presence of the acyclic tail tripeptide in the nonapeptide hormones induces a conformation in the preceding hexapeptide that favours the formation of an intramolecular disulphide bond. For (8-arginine)vasopressin, intramolecular disulphide-bond formation is enhanced by extension of the peptide chain from either the N- or the C-terminus. The possible significance of these studies to neurohypophysial hormone-prohormone relationships is discussed.

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