ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins

Bhat, Aadil Hussain; Mondal, Homchoru; Chauhan, Jagat; Raghava, Gajendra P. S.; Methi, Amrish; Rao, A. V. Subba

doi:10.1093/nar/gkr911

Cited by 25 publications

(19 citation statements)

References 35 publications

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“…In addition, we have recently proposed an agl (archaeal glycosylation)-based protocol for naming relevant new genes associated with archaeal Nglycosylation that would allow the ready identification of commonalities in the pathways among diverse Archaea (61). The interested reader is also directed to the ProGlycProt database (http://www.proglycprot.org/), a repository for bacterial and archaeal glycoproteins with experimentally validated glycosylation sites (62).…”

Section: N-glycosylation Pathways In Archaeal Model Systemsmentioning

confidence: 99%

N-Linked Glycosylation in Archaea: a Structural, Functional, and Genetic Analysis

Jarrell

Ding

Meyer

et al. 2014

Microbiol Mol Biol Rev

184

214

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SUMMARY N-glycosylation of proteins is one of the most prevalent posttranslational modifications in nature. Accordingly, a pathway with shared commonalities is found in all three domains of life. While excellent model systems have been developed for studying N-glycosylation in both Eukarya and Bacteria , an understanding of this process in Archaea was hampered until recently by a lack of effective molecular tools. However, within the last decade, impressive advances in the study of the archaeal version of this important pathway have been made for halophiles, methanogens, and thermoacidophiles, combining glycan structural information obtained by mass spectrometry with bioinformatic, genetic, biochemical, and enzymatic data. These studies reveal both features shared with the eukaryal and bacterial domains and novel archaeon-specific aspects. Unique features of N-glycosylation in Archaea include the presence of unusual dolichol lipid carriers, the use of a variety of linking sugars that connect the glycan to proteins, the presence of novel sugars as glycan constituents, the presence of two very different N-linked glycans attached to the same protein, and the ability to vary the N-glycan composition under different growth conditions. These advances are the focus of this review, with an emphasis on N-glycosylation pathways in Haloferax , Methanococcus , and Sulfolobus .

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Section: N-glycosylation Pathways In Archaeal Model Systemsmentioning

confidence: 99%

N-Linked Glycosylation in Archaea: a Structural, Functional, and Genetic Analysis

Jarrell

Ding

Meyer

et al. 2014

Microbiol Mol Biol Rev

184

214

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“…Glycosyltransferase enzymes employ UDP-, GDP- or CMP-‘activated’ sugars as cofactors, from which they transfer the respective carbohydrate entities onto substrate proteins (Ohtsubo and Marth 2006). Glycosylation is abundant in viruses, prokaryotes, archea and eukaryotes (Vigerust and Shepherd 2007; Eichler and Adams 2005; Bhat et al 2011; Cummings 2009; Khoury et al 2011; Hart and Copeland 2010), where it is involved in nutrient sensing, transcription, translation, signal transduction, organelle transport and cell–cell communication (Roth 2002; Hart et al 2011; Marth and Grewal 2008). Conversely, these functions are often hijacked by pathogens for invasive mechanisms of cell entry (Varki 2008; Vigerust and Shepherd 2007).…”

Section: Glycosylationmentioning

confidence: 99%

Cell signaling, post-translational protein modifications and NMR spectroscopy

et al. 2012

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Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy.

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“…Since, antigenic sites are crucial for pathogenicity and virulence of the microorganism. In this study, we found 16,22,13,14,21,19,25, and 20 putative antigenic sites for MurB, MurE, MraY, MurG, MurD, MurF, MurC, and MurA, respectively and most of the antigenic sites are found in the binding pocket of concerned protein.…”

Section: Prediction Of Functional Domains Subcellular Localization mentioning

confidence: 55%

“…In addition to the above-indicated parameters, the possible post-translation modifications (phosphorylation, glycosylation, and acetylation) sites of Mur family proteins were predicted by using MP Site (microbial phosphorylation site predictor) for phosphorylation [24], GLYCOPP v 1.0 for prediction of glycosylation sites in prokaryotes [25], and GPS-PAIL 2.0 software for acetylation [26].…”

Section: Prediction Of Possible Phosphorylation Glycosylation and Amentioning

confidence: 99%

Prioritization of Mur family drug targets against A. baumannii and identification of their homologous proteins through molecular phylogeny, primary sequence, and structural analysis

Amera

Khan

Jha

et al. 2020

Journal of Genetic Engineering and Biotechnology

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Background: The World Health Organization (WHO) report stated that Acinetobacter baumannii had been classified as one of the most important pathogenic bacteria causing nosocomial infection in hospital patients due to multidrug resistance (MDR). It is vital to find out new bacterial drug targets and annotated their structure and function for the exploration of new anti-bacterial agents. The present study utilized a systematic route to prioritize the potential drug targets that belong to Mur family of Acinetobacter baumannii and identify their homologous proteins using a computational approach such as sequence similarity search, multiple sequence alignment, phylogenetic analysis, protein sequence, and protein structure analysis. Results: From the results of protein sequence analysis of eight Mur family proteins, they divided into three main enzymatic classes namely transferases (MurG, MurA and MraY), ligases (MurC, MurD, MurE, and MurF), and oxidoreductase (MurB). Based on the results of intra-comparative protein sequence analysis and enzymatic classification, we have chosen MurB, MurE, and MurG as the prioritized drug targets from A. baumannii and subjected them for further detailed studies of inter-species comparison. This inter-species comparison help us to explore the sequential and structural properties of homologous proteins in other species and hence, opens a gateway for new target identification and using common inhibitor for different bacterial species caused by various diseases. The pairwise sequence alignment results between A. baumannii's MurB with A. calcoaceticus's MurB, A. baumannii's MurE with A. seifertii's MurE, and A. baumannii's MurG with A. pittii's MurG showed that every group of the proteins are highly similar with each other and they showed sequence identity of 95.7% and sequence similarity of 97.2%. Conclusion: Together with the results of secondary and three-dimensional structure predictions explained that three selected proteins (MurB, MurE, and MurG) from A. baumannii and their related proteins (AcMurB, AsMurE, and ApMurG) belong to mixed αβ class and they are very similar.

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ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins

Cited by 25 publications

References 35 publications

N-Linked Glycosylation in Archaea: a Structural, Functional, and Genetic Analysis

N-Linked Glycosylation in Archaea: a Structural, Functional, and Genetic Analysis

Cell signaling, post-translational protein modifications and NMR spectroscopy

Prioritization of Mur family drug targets against A. baumannii and identification of their homologous proteins through molecular phylogeny, primary sequence, and structural analysis

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