scholarly journals Structure of UBE2K–Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension

2022 ◽  
Author(s):  
Mark A. Nakasone ◽  
Karolina A. Majorek ◽  
Mads Gabrielsen ◽  
Gary J. Sibbet ◽  
Brian O. Smith ◽  
...  
Keyword(s):  
Chain Extension ◽  
Chain Elongation ◽  
Biological Processes ◽  
Binding Modes ◽  
Active Site Residues ◽  
Transient Nature ◽  
Uba Domain ◽  
Chain Synthesis ◽  
Covalently Linked ◽  
Ring E3

AbstractUbiquitin (Ub) chain types govern distinct biological processes. K48-linked polyUb chains target substrates for proteasomal degradation, but the mechanism of Ub chain synthesis remains elusive due to the transient nature of Ub handover. Here, we present the structure of a chemically trapped complex of the E2 UBE2K covalently linked to donor Ub and acceptor K48-linked di-Ub, primed for K48-linked Ub chain synthesis by a RING E3. The structure reveals the basis for acceptor Ub recognition by UBE2K active site residues and the C-terminal Ub-associated (UBA) domain, to impart K48-linked Ub specificity and catalysis. Furthermore, the structure unveils multiple Ub-binding surfaces on the UBA domain that allow distinct binding modes for K48- and K63-linked Ub chains. This multivalent Ub-binding feature serves to recruit UBE2K to ubiquitinated substrates to overcome weak acceptor Ub affinity and thereby promote chain elongation. These findings elucidate the mechanism of processive K48-linked polyUb chain formation by UBE2K.

scholarly journals The E2-25K ubiquitin-associated (UBA) domain aids in polyubiquitin chain synthesis and linkage specificity

2011 ◽  
Vol 405 (4) ◽  
pp. 662-666 ◽  
Author(s):  
Randall C. Wilson ◽  
Stephen P. Edmondson ◽  
Justin W. Flatt ◽  
Kimberli Helms ◽  
Pamela D. Twigg
Keyword(s):  
Polyubiquitin Chain ◽  
Uba Domain ◽  
Chain Synthesis

scholarly journals Molecular Docking Evaluation of Some Natural Phenolic Compounds as Aldose Reductase Inhibitors for Diabetic Complications

2017 ◽  
Vol 5 (2) ◽  
pp. 135-148 ◽  
Author(s):  
Ajmer Singh Grewal ◽  
Neelam Sharma ◽  
Sukhbir Singh ◽  
Sandeep Arora
Keyword(s):  
Molecular Docking ◽  
Aldose Reductase ◽  
Diabetic Complications ◽  
Binding Free Energy ◽  
Docking Study ◽  
Polyol Pathway ◽  
Binding Modes ◽  
Active Site Residues ◽  
Molecular Docking Study ◽  
Natural Phenols

The enzyme aldose reductase (AR) is a member of aldoketoreductase super-family which catalyzes the formation of sorbitol from glucose through polyol pathway of glucose catabolism. Reduced sorbitol production via polyol pathway due to AR inhibition is a target of choice for controlling major complications of diabetes. Epalrestat is the only commercially available inhibitor of AR till date,thus, there is a great need to search for more economical, nontoxic and safer inhibitors of AR enzyme. Flavonoids,the polyphenol compounds in plants have been reported for inhibitory effects against AR. The objective of this study is to explore the binding modes of naturalphenolic compounds with AR to design safer natural drugs as alternatives to synthetic drugs. We conducted a molecular docking study on some naturalphenolic compounds with AR enzyme in complex with the synthetic inhibitor. The overlay of the docked pose of the selected natural phenols with the ARreference inhibitor complex showed that the selected natural compounds have the similar binding pattern with the active site residues of the enzyme as that of co-crystallized inhibitor. The results of docking study showed the best binding affinity of AR with that of 2-(4-hydroxy-3-methoxyphenyl) ethanoic acid and butein, having the lowest binding free energy of –9.8 kcal/mol and–9.7 kcal/mol, respectively. This information can be utilized to design potent, economical and non-toxic natural AR inhibitors from natural phenols for the therapeutics of diabetic complications.

scholarly journals Analysis of the Topology and Active-Site Residues of WbbF, a Putative O-Polysaccharide Synthase from Salmonella enterica Serovar Borreze

2019 ◽  
Vol 202 (5) ◽  
Author(s):  
Samantha S. Wear ◽  
Brittany A. Hunt ◽  
Bradley R. Clarke ◽  
Chris Whitfield
Keyword(s):  
Salmonella Enterica ◽  
Lipid A ◽  
Critical Role ◽  
Cellulose Synthase ◽  
Site Directed Mutagenesis ◽  
Chain Extension ◽  
Active Site Residues ◽  
Content Type ◽  
Membrane Spanning ◽  
And Function

ABSTRACT Bacterial lipopolysaccharides are major components and contributors to the integrity of Gram-negative outer membranes. The more conserved lipid A-core part of this complex glycolipid is synthesized separately from the hypervariable O-antigenic polysaccharide (OPS) part, and they are joined in the periplasm prior to translocation to the outer membrane. Three different biosynthesis strategies are recognized for OPS biosynthesis, and one, the synthase-dependent pathway, is currently confined to a single example: the O:54 antigen from Salmonella enterica serovar Borreze. Synthases are complex enzymes that have the capacity to both polymerize and export bacterial polysaccharides. Although synthases like cellulose synthase are widespread, they typically polymerize a glycan without employing a lipid-linked intermediate, unlike the O:54 synthase (WbbF), which produces an undecaprenol diphosphate-linked product. This raises questions about the overall similarity between WbbF and conventional synthases. In this study, we examine the topology of WbbF, revealing four membrane-spanning helices, compared to the eight in cellulose synthase. Molecular modeling of the glycosyltransferase domain of WbbF indicates a similar architecture, and site-directed mutagenesis confirmed that residues important for catalysis and processivity in cellulose synthase are conserved in WbbF and required for its activity. These findings indicate that the glycosyltransferase mechanism of WbbF and classic synthases are likely conserved despite the use of a lipid acceptor for chain extension by WbbF. IMPORTANCE Glycosyltransferases play a critical role in the synthesis of a wide variety of bacterial polysaccharides. These include O-antigenic polysaccharides, which form the distal component of lipopolysaccharides and provide a protective barrier important for survival and host-pathogen interactions. Synthases are a subset of glycosyltransferases capable of coupled synthesis and export of glycans. Currently, the O:54 antigen of Salmonella enterica serovar Borreze involves the only example of an O-polysaccharide synthase, and its generation of a lipid-linked product differentiates it from classical synthases. Here, we explore features conserved in the O:54 enzyme and classical synthases to shed light on the structure and function of the unusual O:54 enzyme.

Chemical and Biological Evaluation of Thiosemicarbazone-Bearing Heterocyclic Metal Complexes

2020 ◽  
Vol 20 ◽  
Author(s):  
Ana I. Matesanz ◽  
Jorge M. Herrero ◽  
Adoración G. Quiroga
Keyword(s):  
Biological Properties ◽  
Biological Evaluation ◽  
Biological Molecules ◽  
Biological Processes ◽  
Binding Modes ◽  
Future Studies ◽  
Vitamine B12 ◽  
Electronic Delocalization ◽  
Wide Range ◽  
Electronic And Structural Properties

: Thiosemicarbazones (TSCNs) constitute a broad family of compounds (R1R2C=N-NH-C(S)-NR3R4) particularly attractive because many of them display some biological activity against a wide range of microorganisms and cancer cells. Their activity can be related with their electronic and structural properties, which offer a rich set of donor atoms for metal coordination and a high electronic delocalization providing different binding modes for biomolecules. Heterocycles such as pyrrole, imidazole and triazole are present in biological molecules such as Vitamine B12 and amino acids and could potentially target multiple biological processes. Considering this, we have explored the chemistry and biological properties of thiosemicarbazones series and their complexes bearing heterocycles such as pyrrole, imidazole, thiazole and triazole. We focus at the chemistry and cytotoxicity of those derivatives to find out the structure activity relationships, and particularly we analyzed those examples with the TSCN units in which the mechanism of action information has been profoundly studied and pathways determined, to promote future studies for heterocycle derivatives.

Cullin-RING Ubiquitin Ligase Regulatory Circuits: a Quarter Century Beyond the F-box Hypothesis

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
J. Wade Harper ◽  
Brenda A. Schulman
Keyword(s):  
Ubiquitin Ligase ◽  
Annual Review ◽  
Publication Date ◽  
Specific Substrate ◽  
Biological Processes ◽  
Quarter Century ◽  
Cellular Decision Making ◽  
Regulatory Circuits ◽  
Ring E3

Cullin-RING ubiquitin ligases (CRLs) are dynamic modular platforms that regulate myriad biological processes through target-specific ubiquitylation. Our knowledge of this system emerged from the F-box hypothesis, posited a quarter century ago: Numerous interchangeable F-box proteins confer specific substrate recognition for a core CUL1-based RING E3 ubiquitin ligase. This paradigm has been expanded through the evolution of a superfamily of analogous modular CRLs, with five major families and over 200 different substrate-binding receptors in humans. Regulation is achieved by numerous factors organized in circuits that dynamically control CRL activation and substrate ubiquitylation. CRLs also serve as a vast landscape for developing small molecules that reshape interactions and promote targeted ubiquitylation-dependent turnover of proteins of interest. Here, we review molecular principles underlying CRL function, the role of allosteric and conformational mechanisms in controlling substrate timing and ubiquitylation, and how the dynamics of substrate receptor interchange drives the turnover of selected target proteins to promote cellular decision making. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The control of chondroitin sulphate biosynthesis and its influence on the structure of cartilage proteoglycans

1982 ◽  
Vol 202 (2) ◽  
pp. 387-395 ◽  
Author(s):  
D Mitchell ◽  
T Hardingham
Keyword(s):  
Actinomycin D ◽  
Core Protein ◽  
Chondroitin Sulphate ◽  
Chain Elongation ◽  
Chondrosarcoma Cell ◽  
Acceptor Concentration ◽  
The Core ◽  
Chain Synthesis ◽  
Cartilage Proteoglycans ◽  
Elongation Activity

Chondroitin sulphate synthesis on proteoglycans was decreased in rat chondrosarcoma cell cultures in the presence of cycloheximide (0.1-1.0 muM) or p-nitrophenyl beta-D-xyloside (50 microM). In the presence of cycloheximide the proteoglycan monomer was of larger size, the chondroitin sulphate chains were increased in length, but a similar number of chains was attached to each proteoglycan and the size of the core protein was unaltered. In the presence of p-nitrophenyl beta-D-xyloside (50 microM), chondroitin sulphate synthesis was increased (by 60-80%), but the incorporation into proteoglycans was decreased (by 70%). The chondroitin sulphate chains were of shorter length than in control cultured and the number of chains attached to each proteoglycan was decreased. In cultures with cycloheximide or actinomycin D the synthesis of chondroitin sulphate was less inhibited on beta-xyloside than on endogenous proteoglycan. When the rate of chondroitin sulphate synthesis was decreased by lowering the temperature of cultures, the chains synthesized at 22 and 4 degrees C were much longer than at 37 degrees C, but in the presence of p-nitrophenyl beta-D-xyloside the chains were of the same length at all three temperatures. A model of chain elongation is thus proposed in which the rate of chain synthesis is determined by the concentration of xylosyl acceptor and the length of the chains is determined by the ratio of elongation activity to xylosyl-acceptor concentration.

scholarly journals Transition state mimics are valuable mechanistic probes for structural studies with the arginine methyltransferase CARM1

2017 ◽  
Vol 114 (14) ◽  
pp. 3625-3630 ◽  
Author(s):  
Matthijs J. van Haren ◽  
Nils Marechal ◽  
Nathalie Troffer-Charlier ◽  
Agostino Cianciulli ◽  
Gianluca Sbardella ◽  
...  
Keyword(s):  
Transition State ◽  
Active Site ◽  
Arginine Methylation ◽  
Eukaryotic Cells ◽  
Structural Studies ◽  
Potential Therapeutic Target ◽  
Arginine Methyltransferase ◽  
Transient Nature ◽  
The Family ◽  
Covalently Linked

Coactivator associated arginine methyltransferase 1 (CARM1) is a member of the protein arginine methyltransferase (PRMT) family and methylates a range of proteins in eukaryotic cells. Overexpression of CARM1 is implicated in a number of cancers, and it is therefore seen as a potential therapeutic target. Peptide sequences derived from the well-defined CARM1 substrate poly(A)-binding protein 1 (PABP1) were covalently linked to an adenosine moiety as in the AdoMet cofactor to generate transition state mimics. These constructs were found to be potent CARM1 inhibitors and also formed stable complexes with the enzyme. High-resolution crystal structures of CARM1 in complex with these compounds confirm a mode of binding that is indeed reflective of the transition state at the CARM1 active site. Given the transient nature of PRMT–substrate complexes, such transition state mimics represent valuable chemical tools for structural studies aimed at deciphering the regulation of arginine methylation mediated by the family of arginine methyltransferases.

scholarly journals Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C

Cell ◽  
2016 ◽  
Vol 165 (6) ◽  
pp. 1440-1453 ◽  
Author(s):  
Nicholas G. Brown ◽  
Ryan VanderLinden ◽  
Edmond R. Watson ◽  
Florian Weissmann ◽  
Alban Ordureau ◽  
...  
Keyword(s):  
Chain Elongation ◽  
Ubiquitin Chain ◽  
Ring E3 ◽  
Dual Ring

scholarly journals Signal recognition particle causes a transient arrest in the biosynthesis of prepromelittin and mediates its translocation across mammalian endoplasmic reticulum.

1987 ◽  
Vol 104 (1) ◽  
pp. 61-66 ◽  
Author(s):  
I Ibrahimi
Keyword(s):  
Endoplasmic Reticulum ◽  
Wheat Germ ◽  
Signal Recognition Particle ◽  
Chain Elongation ◽  
Translation System ◽  
Signal Recognition ◽  
Nascent Chain ◽  
Reticulocyte Lysate ◽  
The Difference ◽  
Chain Synthesis

The translocation of prepromelittin (pPM) across mammalian endoplasmic reticulum was studied in both wheat germ and reticulocyte lysate. In the wheat germ system, signal recognition particle (SRP) caused a transient arrest in the synthesis of pPM. This was indicated by a slowdown in the rate of synthesis of pPM in the presence of SRP. The arrest was specific, dependent on the concentration of SRP, and more effective at early incubation time. In a tightly synchronized translation system, SRP had no apparent effect on the elongation of pPM, indicating that the effect of SRP on pPM chain synthesis might be at the final stages of chain elongation and release from the ribosome. This was reflected in a transient accumulation of pPM as peptidyl tRNA. Because pPM is composed of only 70 amino acids, arrest by SRP may be very close to chain termination. Arrest at this stage of chain synthesis seems to be unstable and the nascent chain gets terminated and released from the ribosome after a transient delay. The translocation of pPM was shown to be dependent on both SRP and docking protein. The difference in the translocation efficiency of pPM in reticulocyte and wheat germ lysates may reflect a difference in the targeting process in the two systems.

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