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Tim Barrel

Fei Zheng, Josh V Vermaas, Jie Zheng, Yuan Wang, Tao Tu, Xiaoyu Wang, Xiangming Xie, Bin Yao, Gregg T Beckham, Huiying Luo
Cellulases from glycoside hydrolase (GH) family 5 are key endoglucanase enzymes in the degradation of diverse polysaccharide substrates and are used in industrial enzyme cocktails to break down biomass. The GH5 family shares a canonical (βα)8 -barrel structure, where each (βα) module is essential for the enzyme stability and activity. Despite their shared topology, the thermostability of GH5 endoglucanase enzymes can vary significantly, and highly thermostable variants are often sought for industrial applications...
December 14, 2018: Applied and Environmental Microbiology
Maria Rafiq, Ashiq Hussain, Kausar Hussain Shah, Qamar Saeed, Muhammad Umair Sial, Zahid Ali, Friedrich Buck, Richard E Goodman, Binish Khaliq, Uzma Ishaq, Mirza Ahsen Baig, Aisha Munawar, Seema Mahmood, Ahmed Akrem
The present study describes the predicted model and functional characterization of an endochitinase (30 kDa) from corms of Gladiolus grandiflorus. ESI-QTOF-MS generated peptide showed 96% sequence homology with family 18, Class III acidic endochitinase of Gladiolus gandavensis. Purified G. grandiflorus chitinase (GgChi) hydrolyzed 4-methylumbelliferyl β-d-N,N',N''-triacetylchitotriose substrate showing specific endochitinase activity. Since no structural details of GgChi were available in the Protein Data Bank (PDB), a homology model was predicted using the coordinate information of Crocus vernus chitinase (PDB ID: 3SIM)...
December 2018: Kaohsiung Journal of Medical Sciences
Tripti Dadheech, Subhash Jakhesara, Prakram Singh Chauhan, Ramesh Pandit, Ankit Hinsu, Anju Kunjadiya, Dharamshibhai Rank, Chaitanya Joshi
Members of the genus Aspergillus are extensively studied ascomycetes because of their ability to synthesize high value-added compounds and enzymes of industrial interest. Precise whole genome assembly and gene annotation are significant for gene functional analyses. Here, we report the draft genome sequencing, assembly and whole genome analysis of Aspergillus terreus P14_T3, isolated from rumen sample of cattle fed with coconut-coir. A total of 13,340 protein-coding genes were predicted, among them 493 are involved in degradation of complex carbohydrate polysaccharides...
December 3, 2018: International Journal of Biological Macromolecules
M Laura Mascotti, Hemant Kumar, Quoc-Thai Nguyen, Maximiliano Juri Ayub, Marco W Fraaije
During the last decade the number of characterized F420 -dependent enzymes has significantly increased. Many of these deazaflavoproteins share a TIM-barrel fold and are structurally related to FMN-dependent luciferases and monooxygenases. In this work, we traced the origin and evolutionary history of the F420 -dependent enzymes within the luciferase-like superfamily. By a thorough phylogenetic analysis we inferred that the F420 -dependent enzymes emerged from a FMN-dependent common ancestor. Furthermore, the data show that during evolution, the family of deazaflavoproteins split into two well-defined groups of enzymes: the F420 -dependent dehydrogenases and the F420 -dependent reductases...
December 4, 2018: Scientific Reports
Hai Yan Cao, Peng Wang, Ming Peng, Xuan Shao, Xiu Lan Chen, Chun Yang Li
DmoA is a monooxygenase which uses dioxygen (O2 ) and reduced flavin mononucleotide (FMNH2 ) to catalyze the oxidation of dimethylsulfide (DMS). Although it has been characterized, the structure of DmoA remains unknown. Here, the crystal structure of DmoA was determined to a resolution of 2.28 Å and was compared with those of its homologues LadA and BdsA. The results showed that their overall structures are similar: they all share a conserved TIM-barrel fold which is composed of eight α-helices and eight β-strands...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
Tomohiko Matsuzawa, Masahiro Watanabe, Yusuke Nakamichi, Zui Fujimoto, Katsuro Yaoi
Isoprimeverose-producing enzymes (IPases) release isoprimeverose (α-d-xylopyranosyl-(1→6)-d-glucopyranose) from the non-reducing end of xyloglucan oligosaccharides. Aspergillus oryzae IPase (IpeA) is classified as a member of the glycoside hydrolase family 3 (GH3); however, it has unusual substrate specificity compared with other GH3 enzymes. Xylopyranosyl branching at the non-reducing ends of xyloglucan oligosaccharides is vital for IpeA activity. We solved the crystal structure of IpeA with isoprimeverose at 2...
November 13, 2018: Journal of Structural Biology
Katharina Weinhäupl, Caroline Lindau, Audrey Hessel, Yong Wang, Conny Schütze, Tobias Jores, Laura Melchionda, Birgit Schönfisch, Hubert Kalbacher, Beate Bersch, Doron Rapaport, Martha Brennich, Kresten Lindorff-Larsen, Nils Wiedemann, Paul Schanda
The exchange of metabolites between the mitochondrial matrix and the cytosol depends on β-barrel channels in the outer membrane and α-helical carrier proteins in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones escort these proteins through the intermembrane space, but the structural and mechanistic details remain elusive. We have used an integrated structural biology approach to reveal the functional principle of TIM chaperones. Multiple clamp-like binding sites hold the mitochondrial membrane proteins in a translocation-competent elongated form, thus mimicking characteristics of co-translational membrane insertion...
November 15, 2018: Cell
Jay Prakash Kumar, Harshvardhan Rao, Vinod Nayak, S Ramaswamy
N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) to N-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host-pathogen interactions. In this study, atomic resolution structures of NanA from Fusobacterium nucleatum (FnNanA) in ligand-free and ligand-bound forms are reported at 2...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
Tsehai A J Grell, Benjamin N Bell, Chi Nguyen, Daniel P Dowling, Nathan A Bruender, Vahe Bandarian, Catherine L Drennan
7-carboxy-7-deazaguanine synthase, QueE, catalyzes the radical mediated ring contraction of 6-carboxy-5,6,7,8-tetrahydropterin, forming the characteristic pyrrolopyrimidine core of all 7-deazaguanine natural products. QueE is a member of the S-adenosyl-L-methionine (AdoMet) radical enzyme superfamily, which harnesses the reactivity of radical intermediates to perform challenging chemical reactions. Members of the AdoMet radical enzyme superfamily utilize a canonical binding motif, a CX3 CXφC motif, to bind a [4Fe-4S] cluster and a partial (β/α)6 TIM barrel fold for the arrangement of AdoMet and substrates for catalysis...
October 19, 2018: Protein Science: a Publication of the Protein Society
Yusuf Sürmeli, Hüseyin İlgü, Gülşah Şanlı-Mohamed
α-L-Arabinofuranosidase (Abf) is a potential enzyme because of its synergistic effect with other hemicellulases in agro-industrial field. In this study, directed evolution was applied to Abf from Geobacillus vulcani GS90 (GvAbf) using one round error-prone PCR and constructed a library of 73 enzyme variants of GvAbf. The activity screening of the enzyme variants was performed on soluble protein extracts using p-nitrophenyl α-L-arabinofuranoside as substrate. Two high activity displaying variants (GvAbf L307S and GvAbf Q90H/L307S) were selected, purified, partially characterized, and structurally analyzed...
October 17, 2018: Biotechnology and Applied Biochemistry
Hanine Lattouf, Loay Kassem, Julien Jacquemetton, Ali Choucair, Coralie Poulard, Olivier Trédan, Laura Corbo, Mona Diab-Assaf, Nader Hussein, Isabelle Treilleux, Muriel Le Romancer
Protein arginine methyltransferase 5 (PRMT5) is the main enzyme responsible for the symmetrical dimethylation of arginine residues on target proteins in both the cytoplasm and the nucleus. Though its activity has been associated with tumor progression in various cancers, the expression pattern of this oncoprotein has been scarcely studied in breast cancer. In the current work, we analyzed its expression in a large cohort of breast cancer patients, revealing higher nuclear PRMT5 levels in ERα-positive tumors and an association with prolonged disease free and overall survival...
October 5, 2018: International Journal of Cancer. Journal International du Cancer
Bernadette Rubio, Patrick Cosson, Mélodie Caballero, Frédéric Revers, Joy Bergelson, Fabrice Roux, Valérie Schurdi-Levraud
The genetic architecture of plant response to viruses has often been studied in model non-natural pathosystems under controlled conditions. There is an urgent need to elucidate the genetic architecture of the response to viruses in a natural setting. A field experiment was performed in each of two years. In total, 318 Arabidopsis thaliana accessions were inoculated with its natural Turnip mosaic virus (TuMV). The accessions were phenotyped for viral accumulation, frequency of infected plants, stem length and symptoms...
October 3, 2018: New Phytologist
Fredj Ben Bdira, Marta Artola, Herman S Overkleeft, Marcellus Ubbink, Johannes M Aerts
Glycosyl hydrolases (GHs) are carbohydrate-active enzymes that hydrolyze a specific β-glycosidic bond in glycoconjugate substrates; β-glucosidases degrade glucosylceramide, a ubiquitous glycosphingolipid. GHs are grouped into structurally similar families, which themselves can be grouped into clans. GH1, GH5, and GH30 glycosidases belong to clan A hydrolases with a catalytic (β/α)8 TIM barrel domain, whereas GH116 belongs to clan O with a catalytic (α/α)6 domain. In humans, GH abnormalities underlie metabolic diseases...
October 2, 2018: Journal of Lipid Research
Jacob Ball, Renata A G Reis, Johnson Agniswamy, Irene T Weber, Giovanni Gadda
The crystal structure of the NADH:quinone oxidoreductase PA1024 has been solved in complex with NAD+ to 2.2 Å resolution. The nicotinamide C4 is 3.6 Å from the FMN N5 atom, with a suitable orientation for facile hydride transfer. NAD+ binds in a folded conformation at the interface of the TIM-barrel domain and the extended domain of the enzyme. Comparison of the enzyme-NAD+ structure with that of the ligand-free enzyme revealed a different conformation of a short loop (75-86) that is part of the NAD+ -binding pocket...
September 24, 2018: Protein Science: a Publication of the Protein Society
Charles Bou-Nader, Damien Brégeon, Ludovic Pecqueur, Marc Fontecave, Djemel Hamdane
Dihydrouridine (D) is an abundant modified base of tRNA found in the majority of living organisms. This base is synthesized via an NADPH-dependent reduction of specific uridines by the dihydrouridine synthases (Dus), a large family of flavoenzymes comprising eight subfamilies. Almost all of these enzymes function with only two conserved domains, an N-terminal catalytic domain (TBD) adopting a TIM barrel fold and a unique C-terminal helical domain (HD) devoted to tRNA recognition, except for the animal U20-specific Dus2 enzyme...
September 18, 2018: Biochemistry
Mary F Roberts, Hanif M Khan, Rebecca Goldstein, Nathalie Reuter, Anne Gershenson
Phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes from Gram-positive bacteria are secreted virulence factors that aid in downregulating host immunity. These PI-PLCs are minimalist peripheral membrane enzymes with a distorted (βα)8 TIM barrel fold offering a conserved and stable scaffold for the conserved catalytic amino acids while membrane recognition is achieved mostly through variable loops. Decades of experimental and computational research on these enzymes have revealed the subtle interplay between molecular mechanisms of catalysis and membrane binding, leading to a semiquantitative model for how they find, bind, and cleave their respective substrates on host cell membranes...
September 26, 2018: Chemical Reviews
Burkhard Stoffels, Nils Sommer, Christine Berteld, Tim Vilz, Martin von Websky, Jörg C Kalff, Dimitrios Pantelis
INTRODUCTION: Complications following the creation of permanent intestinal ostomies are common and lead to serious problems in the stoma care of affected patients. The aim of this prospective, single-centre follow-up study was to record the rate of late complications in our own patient group and to identify potential risk factors. METHODS: All patients who received a permanent intestinal ostomy in our clinic within the period 2006 - 2016 were included in the study...
August 1, 2018: Zentralblatt Für Chirurgie
Gideon Lapidoth, Olga Khersonsky, Rosalie Lipsh, Orly Dym, Shira Albeck, Shelly Rogotner, Sarel J Fleishman
Automated design of enzymes with wild-type-like catalytic properties has been a long-standing but elusive goal. Here, we present a general, automated method for enzyme design through combinatorial backbone assembly. Starting from a set of homologous yet structurally diverse enzyme structures, the method assembles new backbone combinations and uses Rosetta to optimize the amino acid sequence, while conserving key catalytic residues. We apply this method to two unrelated enzyme families with TIM-barrel folds, glycoside hydrolase 10 (GH10) xylanases and phosphotriesterase-like lactonases (PLLs), designing 43 and 34 proteins, respectively...
July 17, 2018: Nature Communications
Lavanyaa Manjunath, Sai Rohit Guntupalli, Michael J Currie, Rachel A North, Renwick C J Dobson, Vinod Nayak, Ramaswamy Subramanian
Sialic acids are nine-carbon sugars that are found abundantly on the cell surfaces of mammals as glycoprotein or glycolipid complexes. Several Gram-negative and Gram-positive bacteria have the ability to scavenge and catabolize sialic acids to use as a carbon source. This gives them an advantage in colonizing sialic acid-rich environments. The genes of the sialic acid catabolic pathway are generally present as the operon nanAKE. The third gene in the operon encodes the enzyme N-acetylmannosamine-6-phosphate 2-epimerase (NanE), which catalyzes the conversion of N-acetylmannosamine 6-phosphate to N-acetylglucosamine 6-phosphate, thus committing it to enter glycolysis...
July 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
D Sean Froese, Jolanta Kopec, Elzbieta Rembeza, Gustavo Arruda Bezerra, Anselm Erich Oberholzer, Terttu Suormala, Seraina Lutz, Rod Chalk, Oktawia Borkowska, Matthias R Baumgartner, Wyatt W Yue
The folate and methionine cycles are crucial for biosynthesis of lipids, nucleotides and proteins, and production of the methyl donor S-adenosylmethionine (SAM). 5,10-methylenetetrahydrofolate reductase (MTHFR) represents a key regulatory connection between these cycles, generating 5-methyltetrahydrofolate for initiation of the methionine cycle, and undergoing allosteric inhibition by its end product SAM. Our 2.5 Å resolution crystal structure of human MTHFR reveals a unique architecture, appending the well-conserved catalytic TIM-barrel to a eukaryote-only SAM-binding domain...
June 11, 2018: Nature Communications
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