scholarly journals Structural Consideration of the Working Mechanism of Fold Type I Transaminases From Eubacteria: Overt and Covert Movement

2019 ◽  
Vol 17 ◽  
pp. 1031-1039 ◽  
Author(s):  
Sunghark Kwon ◽  
Hyun Ho Park
Biochemistry ◽  
2009 ◽  
Vol 48 (5) ◽  
pp. 941-950 ◽  
Author(s):  
Seiji Okazaki ◽  
Atsuo Suzuki ◽  
Tsunehiro Mizushima ◽  
Takeshi Kawano ◽  
Hidenobu Komeda ◽  
...  
Keyword(s):  
Type I ◽  

2006 ◽  
Vol 396 (3) ◽  
pp. 499-507 ◽  
Author(s):  
Yu Yoshikane ◽  
Nana Yokochi ◽  
Kouhei Ohnishi ◽  
Hideyuki Hayashi ◽  
Toshiharu Yagi

Pyridoxamine–pyruvate aminotransferase is a PLP (pyridoxal 5′-phosphate) (a coenzyme form of vitamin B6)-independent aminotransferase which catalyses a reversible transamination reaction between pyridoxamine and pyruvate to form pyridoxal and L-alanine. The gene encoding the enzyme has been identified, cloned and overexpressed for the first time. The mlr6806 gene on the chromosome of a symbiotic nitrogen-fixing bacterium, Mesorhizobium loti, encoded the enzyme, which consists of 393 amino acid residues. The primary sequence was identical with those of archaeal aspartate aminotransferase and rat serine–pyruvate aminotransferase, which are PLP-dependent aminotransferases. The results of fold-type analysis and the consensus amino acid residues found around the active-site lysine residue identified in the present study showed that the enzyme could be classified into class V aminotransferases of fold type I or the AT IV subfamily of the α family of the PLP-dependent enzymes. Analyses of the absorption and CD spectra of the wild-type and point-mutated enzymes showed that Lys197 was essential for the enzyme activity, and was the active-site lysine residue that corresponded to that found in the PLP-dependent aminotransferases, as had been suggested previously [Hodsdon, Kolb, Snell and Cole (1978) Biochem. J. 169, 429–432]. The Kd value for pyridoxal determined by means of CD was 100-fold lower than the Km value for it, suggesting that Schiff base formation between pyridoxal and the active-site lysine residue is partially rate determining in the catalysis of pyridoxal. The active-site structure and evolutionary aspects of the enzyme are discussed.


2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Teresa Milano ◽  
Sebastiana Angelaccio ◽  
Angela Tramonti ◽  
Martino Luigi Di Salvo ◽  
Roberto Contestabile ◽  
...  

The MocR bacterial transcriptional regulators are characterized by an N-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (wHTH) architecture responsible for DNA recognition and binding, linked to a large C-terminal domain (350 residues on average) that is homologous to fold type-I pyridoxal 5′-phosphate (PLP) dependent enzymes like aspartate aminotransferase (AAT). These regulators are involved in the expression of genes taking part in several metabolic pathways directly or indirectly connected to PLP chemistry, many of which are still uncharacterized. A bioinformatics analysis is here reported that studied the features of a distinct group of MocR regulators predicted to be functionally linked to a family of homologous genes coding for integral membrane proteins of unknown function. This group occurs mainly in the Actinobacteria and Gammaproteobacteria phyla. An analysis of the multiple sequence alignments of their wHTH and AAT domains suggested the presence of specificity-determining positions (SDPs). Mapping of SDPs onto a homology model of the AAT domain hinted at possible structural/functional roles in effector recognition. Likewise, SDPs in wHTH domain suggested the basis of specificity of Transcription Factor Binding Site recognition. The results reported represent a framework for rational design of experiments and for bioinformatics analysis of other MocR subgroups.


Extremophiles ◽  
2014 ◽  
Vol 18 (3) ◽  
pp. 589-602 ◽  
Author(s):  
Yuki Uchida ◽  
Hideyuki Hayashi ◽  
Tsubasa Washio ◽  
Ryo Yamasaki ◽  
Shiro Kato ◽  
...  

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 438
Author(s):  
Angela Tramonti ◽  
Roberto Contestabile ◽  
Rita Florio ◽  
Caterina Nardella ◽  
Anna Barile ◽  
...  

Cysteine sulfinic acid decarboxylase catalyzes the last step of taurine biosynthesis in mammals, and belongs to the fold type I superfamily of pyridoxal-5′-phosphate (PLP)-dependent enzymes. Taurine (2-aminoethanesulfonic acid) is the most abundant free amino acid in animal tissues; it is highly present in liver, kidney, muscle, and brain, and plays numerous biological and physiological roles. Despite the importance of taurine in human health, human cysteine sulfinic acid decarboxylase has been poorly characterized at the biochemical level, although its three-dimensional structure has been solved. In the present work, we have recombinantly expressed and purified human cysteine sulfinic acid decarboxylase, and applied a simple spectroscopic direct method based on circular dichroism to measure its enzymatic activity. This method gives a significant advantage in terms of simplicity and reduction of execution time with respect to previously used assays, and will facilitate future studies on the catalytic mechanism of the enzyme. We determined the kinetic constants using L-cysteine sulfinic acid as substrate, and also showed that human cysteine sulfinic acid decarboxylase is capable to catalyze the decarboxylation—besides its natural substrates L-cysteine sulfinic acid and L-cysteic acid—of L-aspartate and L-glutamate, although with much lower efficiency.


2019 ◽  
Vol 73 (6) ◽  
pp. 1-5
Author(s):  
Bożena Kosztyła-Hojna ◽  
Jarosław Łuczaj ◽  
Greta Berger ◽  
Emilia Duchnowska ◽  
Maciej Zdrojkowski ◽  
...  

Introduction: CO2 laser endoscopic cordectomy is the method of laryngeal cancer treatment. The type of cordectomy (I–VI) depends on the extent of the tumor. Endoscopic laser surgery provides more satisfactory phonation conditions in comparison to open surgical procedures. The aim of the study was to classify phonatory compensation mechanisms after CO2 laser cordectomy using the HSDI. Material and methods: The study included 30 men treated and diagnosed at the Department of Otolaryngology and Department of Clinical Phonoaudiology and Logopedics, Medical University of Bialystok. The control included 30 men with no pathological changes in the larynx. Type III, IV and Va CO2 laser cordectomy have been for glottis cancer treatment. Postoperative evaluation has been conducted 6 months after the surgery. HSDI has been used in larynx visualization. Results: Type I compensation occurs most frequently in patients after type III cordectomy. Advanced glottis cancer, as an indication for type IV and V cordectomy, leads to epiglottic hyperfunction and phonation involving vestibular folds – type II and III compensation. Type IV compensation is most frequent in type IV cordectomy. Conclusions: The type compensation is connected with the extent of glottis resection. In cordectomy including anterior commissure and the part of opposite fold (type Va), supraglottic hyperfunction with the participation of vestibular folds (type II and III compensation) has been recorded. Transmuscular cordectomy (type III) most often resulted in type I compensation. Type III-Va cordectomy caused reduction or absence of MW, decrease in amplitude and aperiodicity of vibrations in HSDI.


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