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Amino Acid Similarity (amino + acid_similarity)

Distribution by Scientific Domains

Life Sciences	50%

Selected Abstracts

Cellulases of Penicillium verruculosum

BIOTECHNOLOGY JOURNAL, Issue 8 2010
Valeria V. Morozova
Abstract Nine major cellulolytic enzymes were isolated from a culture broth of a mutant strain of the fungus Penicillium verruculosum: five endo-1, 4-,-glucanases (EGs) having molecular masses 25, 33, 39, 52, and 70 kDa, and four cellobiohydrolases (CBHs: 50, 55, 60, and 66 kDa). Based on amino acid similarities of short sequenced fragments and peptide mass fingerprinting, the isolated enzymes were preliminary classified into different families of glycoside hydrolases: Cel5A (EG IIa, 39 kDa), Cel5B (EG IIb, 33 kDa), Cel6A (CBH II, two forms: 50 and 60 kDa), Cel7A (CBH I: 55 and 66 kDa), Cel7B (EG I: 52 and 70 kDa). The 25 kDa enzyme was identical to the previously isolated Cel12A (EG III). The family assignment was further confirmed by the studies of the substrate specificity of the purified enzymes. High-molecular-weight forms of the Cel6A, Cel7A, and Cel7B were found to possess a cellulose-binding module (CBM), while the catalytically active low-molecular-weight forms of the enzymes, as well as other cellulases, lacked the CBM. Properties of the isolated enzymes, such as substrate specificity toward different polysaccharides and synthetic glycosides, effect of pH and temperature on the enzyme activity and stability, adsorption on Avicel cellulose and kinetics of its hydrolysis, were investigated. [source]

Identification and characterization of a new gene from Variovorax paradoxus Iso1 encoding N -acyl- d -amino acid amidohydrolase responsible for d -amino acid production

FEBS JOURNAL, Issue 19 2002
Pei-Hsun Lin
An N -acyl- d -amino acid amidohydrolase (N -D-AAase) was identified in cell extracts of a strain, Iso1, isolated from an environment containing N -acetyl- d -methionine. The bacterium was classified as Variovorax paradoxus by phylogenetic analysis. The gene was cloned and sequenced. The gene consisted of a 1467-bp ORF encoding a polypeptide of 488 amino acids. The V. paradoxusN -D-AAase showed significant amino acid similarity to the N -acyl- d -amino acid amidohydrolases of the two eubacteria Alcaligenes xylosoxydans A-6 (44,56% identity), Alcaligenes facelis DA1 (54% identity) and the hyperthermophilic archaeon Pyrococcus abyssi (42% identity). After over-expression of the N -D-AAase protein in Escherichia coli, the enzyme was purified by multistep chromatography. The native molecular mass was 52.8 kDa, which agreed with the predicted molecular mass of 52 798 Da and the enzyme appeared to be a monomer protein by gel-filtration chromatography. A homogenous protein with a specific activity of 516 U·mg,1 was finally obtained. After peptide sequencing by LC/MS/MS, the results were in agreement with the deduced amino acid sequence of the N -D-AAase. The pI of the enzyme was 5.12 and it had an optimal pH and temperature of 7.5 and 50 °C, respectively. After 30 min heat treatment at 45 °C, between pH 6 and pH 8, 80% activity remained. The N -D-AAase had higher hydrolysing activity against N -acetyl- d -amino acid derivates containing d -methionine, d -leucine and d -alanine and against N -chloroacetyl- d -phenylalanine. Importantly, the enzyme does not act on the N -acetyl- l -amino acid derivatives. The enzyme was inhibited by chelating agents and certain metal ions, but was activated by 1 mm of Co2+ and Mg2+. Thus, the N -D-AAase from V. paradoxus can be considered a chiral specific and metal-dependent enzyme. [source]

Transcriptional analysis of the gdhA gene in Streptococcus thermophilus

JOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2009
C. Lazzi
Abstract Aims:, To study the transcriptional analysis of glutamate dehydrogenase gene, involved in the amino acid conversion to aroma compound in Streptococcus thermophilus. Methods and Results:, Analysis of the gdhA gene nucleotide sequence of S. thermophilus CNRZ1066 revealed that the coding region is 1353 nucleotides long. The deduced amino acids sequence exhibits the putative GDH active site and some conserved domains characteristic of family I of hexameric GDHs. Phylogenetic analysis revealed that the gdh gene of S. thermophilus clustered with the orthologues of other streptococci such as Streptococcus mutans, Streptococcus agalactiae and Streptococcus infantarius. Studying the structural organization of the gdhA locus the amino acid similarity of GDHs was higher than 87%, but the locus organization was not conserved. A dominant transcript of approximately 1·4 kbp was revealed by Northern blot hybridization, suggesting that gdhA mRNA is monocystronic. Primer extension showed that transcription start point of gdhA was localized 43 bp upstream of the potential start codon (ATG). Conclusions:, The gdhA represents a monocistronic operon highly conserved in phylogenetic-related bacteria. Significance and Impact of the Study:, A deeper knowledge of gdh transcriptional mechanisms could lead to develop S. thermophilus industrial starter cultures with optimized aromatic properties. [source]

Ultrastructure of activated mouse platelets: A qualitative scanning electron microscopy study

MICROSCOPY RESEARCH AND TECHNIQUE, Issue 6 2008
E. Pretorius
Abstract Platelets form an integral part of the coagulation process, and their ultrastructure can provide valuable information regarding diseases associated with hemostasis. During coagulation, platelets aggregate; this aggregation can be achieved in vitro, by adding thrombin to platelet-rich plasma. Previous research showed that human thrombin could be used successfully to activate mouse platelets. When conservative changes are included, the amino acid similarity between human and mouse thrombin is ,75%. In this qualitative study, we compare the ultrastructure of mouse platelet aggregates activated by human thrombin as well as two concentrations of mouse thrombin, using the scanning electron microscope. Results show that both human and mouse thrombin activate platelets to form aggregates with typical pseudopodia formation. Magnification up to 250,000× showed membrane morphology with the open canalicular system pores visible in both the mouse- and human-activated platelets. It is therefore concluded that mouse platelets can be successfully aggregated using either mouse or human thrombin. Microsc. Res. Tech. 2008. © 2008 Wiley-Liss, Inc. [source]