The amino acid sequences of the carbohydrate-binding peptides of various di-N-acetylchitobiose-binding lectins

1992 ◽  
Vol 11 (4) ◽  
pp. 396-397
Author(s):  
Yukiko Konami ◽  
Kazuo Yamamoto ◽  
Toshiaki Osawa ◽  
Taturo Irimura
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Carbohydrate Binding ◽  
Binding Peptides

scholarly journals Prediction of Carbohydrate-Binding Proteins from Sequences Using Support Vector Machines

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Seizi Someya ◽  
Masanori Kakuta ◽  
Mizuki Morita ◽  
Kazuya Sumikoshi ◽  
Wei Cao ◽  
...  
Keyword(s):  
Amino Acid ◽  
Support Vector Machines ◽  
Binding Proteins ◽  
Prediction Method ◽  
Amino Acid Sequences ◽  
Support Vector ◽  
Carbohydrate Binding ◽  
Genome Database ◽  
Vector Machines ◽  
Carbohydrate Binding Proteins

Carbohydrate-binding proteins are proteins that can interact with sugar chains but do not modify them. They are involved in many physiological functions, and we have developed a method for predicting them from their amino acid sequences. Our method is based on support vector machines (SVMs). We first clarified the definition of carbohydrate-binding proteins and then constructed positive and negative datasets with which the SVMs were trained. By applying the leave-one-out test to these datasets, our method delivered 0.92 of the area under the receiver operating characteristic (ROC) curve. We also examined two amino acid grouping methods that enable effective learning of sequence patterns and evaluated the performance of these methods. When we applied our method in combination with the homology-based prediction method to the annotated human genome database, H-invDB, we found that the true positive rate of prediction was improved.

scholarly journals Novel Bifunctional α-l-Arabinofuranosidase/Xylobiohydrolase (ABF3) from Penicillium purpurogenum

2010 ◽  
Vol 76 (15) ◽  
pp. 5247-5253 ◽  
Author(s):  
Mar�a Cristina Ravanal ◽  
Eduardo Callegari ◽  
Jaime Eyzaguirre
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Glycosyl Hydrolase ◽  
Biochemical Properties ◽  
Amino Acid Sequences ◽  
Mass Spectrometry Analysis ◽  
Carbohydrate Binding ◽  
Penicillium Purpurogenum ◽  
Spectrometry Analysis ◽  
Amino Terminal

ABSTRACT The soft rot fungus Penicillium purpurogenum grows on a variety of natural substrates and secretes various isoforms of xylanolytic enzymes, including three arabinofuranosidases. This work describes the biochemical properties as well as the nucleotide and amino acid sequences of arabinofuranosidase 3 (ABF3). This enzyme has been purified to homogeneity. It is a glycosylated monomer with a molecular weight of 50,700 and can bind cellulose. The enzyme is active with p-nitrophenyl α-l-arabinofuranoside and p-nitrophenyl β-d-xylopyranoside with a Km of 0.65 mM and 12 mM, respectively. The enzyme is active on xylooligosaccharides, yielding products of shorter length, including xylose. However, it does not hydrolyze arabinooligosaccharides. When assayed with polymeric substrates, little arabinose is liberated from arabinan and debranched arabinan; however, it hydrolyzes arabinose and releases xylooligosaccharides from arabinoxylan. Sequencing both ABF3 cDNA and genomic DNA reveals that this gene does not contain introns and that the open reading frame is 1,380 nucleotides in length. The deduced mature protein is composed of 433 amino acids residues and has a calculated molecular weight of 47,305. The deduced amino acid sequence has been validated by mass spectrometry analysis of peptides from purified ABF3. A total of 482 bp of the promoter were sequenced; putative binding sites for transcription factors such as CreA (four), XlnR (one), and AreA (three) and two CCAAT boxes were found. The enzyme has two domains, one similar to proteins of glycosyl hydrolase family 43 at the amino-terminal end and a family 6 carbohydrate binding module at the carboxyl end. ABF3 is the first described modular family 43 enzyme from a fungal source, having both α-l-arabinofuranosidase and xylobiohydrolase functionalities.

Differences in amino acid sequences of mistletoe lectin I and III B-subunits determining carbohydrate binding specificity

2004 ◽  
Vol 1675 (1-3) ◽  
pp. 155-164 ◽  
Author(s):  
Irina B. Pevzner ◽  
Igor I. Agapov ◽  
Hideaki Niwa ◽  
Natalia V. Maluchenko ◽  
Mikhail M. Moisenovich ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Specificity ◽  
Amino Acid Sequences ◽  
Carbohydrate Binding ◽  
Mistletoe Lectin ◽  
B Subunits

scholarly journals Cloning, Sequencing, and Expression of a Eubacterium cellulosolvens 5 Gene Encoding an Endoglucanase (Cel5A) with Novel Carbohydrate-Binding Modules, and Properties of Cel5A

2005 ◽  
Vol 71 (10) ◽  
pp. 5787-5793 ◽  
Author(s):  
Kazutoyo Yoda ◽  
Atsushi Toyoda ◽  
Yoshihiro Mukoyama ◽  
Yutaka Nakamura ◽  
Hajime Minato
Keyword(s):  
Amino Acid ◽  
Sequence Similarity ◽  
Glycosyl Hydrolase ◽  
Amino Acid Sequences ◽  
Substrate Affinity ◽  
Carbohydrate Binding ◽  
Gene Encoding ◽  
Carbohydrate Binding Modules ◽  
Hydrolytic Activities ◽  
Eubacterium Cellulosolvens

ABSTRACT A novel Eubacterium cellulosolvens 5 gene encoding an endoglucanase (Cel5A) was cloned and expressed in Escherichia coli, and its enzymatic properties were characterized. The cel5A gene consists of a 3,444-bp open reading frame and encodes a 1,148-amino-acid protein with a molecular mass of 127,047 Da. Cel5A is a modular enzyme consisting of an N-terminal signal peptide, two glycosyl hydrolase family 5 catalytic modules, two novel carbohydrate-binding modules (CBMs), two linker sequences, and a C-terminal sequence with an unknown function. The amino acid sequences of the two catalytic modules and the two CBMs are 94% and 73% identical to each other, respectively. Two regions that consisted of one CBM and one catalytic module were tandemly connected via a linker sequence. The CBMs did not exhibit significant sequence similarity with any other CBMs. Analyses of the hydrolytic activity of the recombinant Cel5A (rCel5A) comprising the CBMs and the catalytic modules showed that the enzyme is an endoglucanase with activities with carboxymethyl cellulose, lichenan, acid-swollen cellulose, and oat spelt xylan. To investigate the functions of the CBMs and the catalytic modules, truncated derivatives of rCel5A were constructed and characterized. There were no differences in the hydrolytic activities with various polysaccharides or in the hydrolytic products obtained from cellooligosaccharides between the two catalytic modules. Both CBMs had the same substrate affinity with intact rCel5A. Removal of the CBMs from rCel5A reduced the catalytic activities with various polysaccharides remarkably. These observations show that CBMs play an important role in the catalytic function of the enzyme.

Characteristics of adjacent family 6 acetylxylan esterases fromFibrobacter succinogenesand the interaction with the Xyn10E xylanase in hydrolysis of acetylated xylan

2005 ◽  
Vol 51 (10) ◽  
pp. 821-832 ◽  
Author(s):  
Dong Keun Kam ◽  
Hyun-Sik Jun ◽  
Jong K Ha ◽  
G Douglas Inglis ◽  
Cecil W Forsberg
Keyword(s):  
Amino Acid ◽  
Plant Cell Wall ◽  
Catalytic Domain ◽  
Amino Acid Sequences ◽  
Carbohydrate Binding ◽  
Fibrobacter Succinogenes ◽  
Acetylxylan Esterase ◽  
Low K ◽  
Hydrolysis Of ◽  
Improve Access

Acetylxylan esterase genes axe6A and axe6B located adjacent to one another on a Fibrobacter succinogenes chromosome have been separately cloned and their properties characterized. The corresponding esterases contained an N-terminal carbohydrate esterase family 6 catalytic domain (CD) and a C-terminal family 6 carbohydrate-binding module (CBM). The amino acid sequences of the CDs and CBMs were found to exhibit 52% and 40% amino acid similarity, respectively. The CDs of the two esterases exhibited the highest similarity to CDs of acetylxylan esterases: AxeA from the ruminal fungi Orpinomyces sp. and BnaA from Neocallimastix patriciarum. Axe6A and Axe6B were optimally active at neutral pH and had low Kmvalues of 0.084 and 0.056 mmol·L–1, respectively. Axe6A and Axe6B were shown to bind to insoluble cellulose and xylan and to soluble arabinoxylan. Axe6A deacetylated acetylated xylan at the same initial rate in the presence and absence of added Xyn10E xylanase from F. succinogenes, but the action of the xylanase on acetylated xylan was dependent upon the initial activity of Axe6A. The capacity of acetylxylan esterases to bind to plant cell wall polymers and to independently deacetylate xylan enabling xylanase to release xylooligo saccharides, documents the central role these enzymes have to improve access of F. succinogenes to cellulose.Key words: Fibrobacter succinogenes S85, acetylxylan esterase, xylanase, synergy.

Cloning of the cycloisomaltotetraose forming-enzymes using whole genome sequence analyses of Agreia sp. D1110 and Microbacterium trichothecenolyticum D2006

2021 ◽  
Author(s):  
Akihiro Fujita ◽  
Akira Kawashima ◽  
Yuji Noguchi ◽  
Shuichi Hirose ◽  
Noriaki Kitagawa ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Draft Genome ◽  
Amino Acid Sequences ◽  
Whole Genome Sequence ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Whole Genome ◽  
Sequence Analyses ◽  
Terminal Amino

Abstract We performed whole genome sequence analyses of Agreia sp. D1110 and Microbacterium trichothecenolyticum D2006 that secrete enzymes to produce cyclo-{→6)-α-d-Glcp-(1→6)-α-d-Glcp-(1→6)-α-d-Glcp-(1→6)-α-d-Glcp-(1→} (CI4) from dextran. Full-length amino acid sequences of CI4-forming enzymes were identified by matching known N-terminal amino acid sequences with products of the draft genome. Domain searches revealed that the CI4-forming enzymes are composed of Glycoside Hydrolase family 66 (GH66) domain, Carbohydrate Binding Module family 35 (CBM35) domain and CBM13 domain, categorizing the CI4-forming enzymes in the GH66. Furthermore, the amino acid sequences of the two CI4-forming enzymes were 71% similar to each other and up to 51% similar to cycloisomaltooligosaccharide glucanotransferases (CITases) categorized in GH66. Differences in sequence between the CI4-forming enzymes and the CITases suggest mechanisms to produce specific cycloisomaltooligosaccharides, and whole genome sequence analyses identified a gene cluster whose gene products likely work in concert with the CI4-forming enzymes.

Identification of H-2Kb-, Db- and Dd-binding peptides derived from amino acid sequences of polyoma virus T antigens

1993 ◽  
Vol 54 (6) ◽  
pp. 992-995 ◽  
Author(s):  
Git Reinholdsson-Ljunggren ◽  
Lars Franksson ◽  
Tina Dalianis ◽  
Hans-Gustaf Ljunggren
Keyword(s):  
Amino Acid ◽  
Polyoma Virus ◽  
Amino Acid Sequences ◽  
T Antigens ◽  
Binding Peptides

Platinum-binding peptides: understanding of selective binding and multifunctionality

2022 ◽  
Author(s):  
Nuttanit Pramounmat ◽  
Katherine Yan ◽  
Jadon Wolf ◽  
Julie Renner
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Interdisciplinary Research ◽  
Amino Acid Sequences ◽  
Selective Binding ◽  
Surface Recognition ◽  
Current State ◽  
Binding Peptides ◽  
Present Understanding

Abstract Platinum-binding peptides have been used for fabrication of complex platinum nanomaterials such as catalysts, metallopharmaceuticals, and electrodes. In this review, we present understanding of the mechanisms behind platinum-binding (Pt-binding) peptides and the applications of the peptides as multifunctional biomaterials. We discuss how the surface recognition, the roles of individual amino acids, and arrangement of amino acid sequences interplay. Our summary on the current state of understanding of Pt-binding peptides highlights opportunities for interdisciplinary research which will expand the applicability of these multifunctional Pt-binding peptides.

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