HHrep is a web server for the de novo identification of repeats in protein sequences, which is based on the pairwise comparison of profile hidden Markov models (HMMs). Its main strength is its sensitivity, allowing it to detect highly divergent repeat units in protein sequences whose repeats could as yet only be detected from their structures. Examples include sequences with beta-propellor fold, ferredoxin-like fold, double psi barrels or (betaalpha)8 (TIM) barrels. We illustrate this with proteins from four superfamilies of TIM barrels by revealing a clear 4- and 8-fold symmetry, which we detect solely from their sequences. This symmetry might be the trace of an ancient origin through duplication of a betaalphabetaalpha or betaalpha unit. HHrep can be accessed at http://hhrep.tuebingen.mpg.de.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538828 | PMC |
| http://dx.doi.org/10.1093/nar/gkl130 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Structural and functional snapshots of a broad-specificity endoglucanase from Thermogutta terrifontis for biomass saccharification.
Arch Biochem Biophys
December 2024
The Division of Structural Biology, The Nuffield Department of Medicine, University of Oxford, UK; The Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0QS, UK. Electronic address:
Multifunctionality, processivity, and thermostability are critical for the cost-effective enzymatic saccharification of non-food plant biomass polymers such as β-glucans, celluloses, and xylans to generate biofuels and other valuable products. We present molecular insights into a processive multifunctional endo-1,3-1,4-β-d-glucanase (Tt_End5A) from the hyperthermophilic bacterium Thermogutta terrifontis. Tt_End5A demonstrated activities against a broad spectrum of β-polysaccharides, including barley glucan, lichenan, carboxymethyl cellulose, regenerated amorphous cellulose (RAC), Avicel, xylan, laminarin, mannan, curdlan, xanthan, and various chromogenic substrates at pH 7 and temperatures ranging from 70 to 80°C.
View Article and Find Full Text PDFBiochemical Characterization of a β-1,3-Glucanase from sp. Having Transglycosylase Activity Suitable to Synthesize β-Glucooligosaccharides.
J Agric Food Chem
December 2024
School of Life Sciences, Shanghai University, Shanghai 200444, China.
β-1,3-Glucanases have prospective applications in areas such as functional oligosaccharide preparation, plant protection, and breweries. In this study, a glycoside hydrolase (GH) family 17 β-1,3-glucanase (BbGlc17A) from bacterium from a microbial mat metagenome from the Great Salt Lake was identified. BbGlc17A catalyzed the hydrolytic conversion of laminarin into β-glucooligosaccharides with polymerization degrees of 3-8.
View Article and Find Full Text PDFEfficient Biotransformation of Icariin to Baohuoside I Using Two Novel GH1 β-Glucosidases.
Molecules
November 2024
School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
(EF) is a traditional Chinese herbal medicine, and its primary bioactive ingredients, such as icariin, are flavonoid glycosides. A rare EF flavonoid, baohuoside I, exhibits superior bioactivities and enhanced bioavailability compared to its metabolic precursor icariin. The biotransformation of icariin to baohuoside I can be effectively and specifically achieved by β-glucosidases.
View Article and Find Full Text PDFStructure and identification of the native PLP synthase complex from lysate.
mBio
January 2025
Department of Microbiology, Immunology & Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA.
Many protein-protein interactions behave differently in biochemically purified forms as compared to their states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, , toward a model methanogenic archaeon.
View Article and Find Full Text PDFStructural, biophysical, and biochemical insights into C-S bond cleavage by dimethylsulfone monooxygenase.
Proc Natl Acad Sci U S A
November 2024
Department of Chemistry, University of Massachusetts, Boston, MA 02125.
Sulfur is an essential element for life. Bacteria can obtain sulfur from inorganic sulfate; but in the sulfur starvation-induced response, employ two-component flavin-dependent monooxygenases (TC-FMOs) from the and operons to assimilate sulfur from environmental compounds including alkanesulfonates and dialkylsulfones. Here, we report binding studies of oxidized FMN to enzymes involved within the enzymatic pathway responsible for converting dimethylsulfone (DMSO) to sulfite.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!