scholarly journals p-Hydroxybenzoate Hydroxylase from Pseudomonas fluorescens. 2. Fitting of the Amino-Acid Sequence to the Tertiary Structure

1983 ◽  
Vol 133 (1) ◽  
pp. 109-118 ◽  
Author(s):  
Wicher J. WEIJER ◽  
Jan HOFSTEENGE ◽  
Jaap J. BEINTEMA ◽  
Rik K. WIERENGA ◽  
Jan DRENTH
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Pseudomonas Fluorescens ◽  
Tertiary Structure ◽  
Hydroxybenzoate Hydroxylase

scholarly journals Catalytic and Molecular Properties of the Quinohemoprotein Tetrahydrofurfuryl Alcohol Dehydrogenase from Ralstonia eutropha Strain Bo

2001 ◽  
Vol 183 (6) ◽  
pp. 1954-1960 ◽  
Author(s):  
Grit Zarnt ◽  
Thomas Schräder ◽  
Jan R. Andreesen
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Alcohol Dehydrogenase ◽  
Tertiary Structure ◽  
Ralstonia Eutropha ◽  
Signal Sequence ◽  
Substrate Inhibition ◽  
Catalytic Efficiency ◽  
Gene Encoding

ABSTRACT The quinohemoprotein tetrahydrofurfuryl alcohol dehydrogenase (THFA-DH) from Ralstonia eutropha strain Bo was investigated for its catalytic properties. The apparentk cat/Km andK i values for several substrates were determined using ferricyanide as an artificial electron acceptor. The highest catalytic efficiency was obtained with n-pentanol exhibiting a k cat/Km value of 788 × 104 M−1 s−1. The enzyme showed substrate inhibition kinetics for most of the alcohols and aldehydes investigated. A stereoselective oxidation of chiral alcohols with a varying enantiomeric preference was observed. Initial rate studies using ethanol and acetaldehyde as substrates revealed that a ping-pong mechanism can be assumed for in vitro catalysis of THFA-DH. The gene encoding THFA-DH from R. eutropha strain Bo (tfaA) has been cloned and sequenced. The derived amino acid sequence showed an identity of up to 67% to the sequence of various quinoprotein and quinohemoprotein dehydrogenases. A comparison of the deduced sequence with the N-terminal amino acid sequence previously determined by Edman degradation analysis suggested the presence of a signal sequence of 27 residues. The primary structure of TfaA indicated that the protein has a tertiary structure quite similar to those of other quinoprotein dehydrogenases.

scholarly journals A DyP-Type Peroxidase of Pleurotus sapidus with Alkene Cleaving Activity

Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1536
Author(s):  
Nina-Katharina Krahe ◽  
Ralf G. Berger ◽  
Franziska Ersoy
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Peroxidase Activity ◽  
Tertiary Structure ◽  
Sulphonic Acid ◽  
Anthraquinone Dyes ◽  
Cleavage Activity ◽  
Pleurotus Sapidus ◽  
Β Carotene

Alkene cleavage is a possibility to generate aldehydes with olfactory properties for the fragrance and flavor industry. A dye-decolorizing peroxidase (DyP) of the basidiomycete Pleurotus sapidus (PsaPOX) cleaved the aryl alkene trans-anethole. The PsaPOX was semi-purified from the mycelium via FPLC, and the corresponding gene was identified. The amino acid sequence as well as the predicted tertiary structure showed typical characteristics of DyPs as well as a non-canonical Mn2+-oxidation site on its surface. The gene was expressed in Komagataella pfaffii GS115 yielding activities up to 142 U/L using 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) as substrate. PsaPOX exhibited optima at pH 3.5 and 40 °C and showed highest peroxidase activity in the presence of 100 µM H2O2 and 25 mM Mn2+. PsaPOX lacked the typical activity of DyPs towards anthraquinone dyes, but oxidized Mn2+ to Mn3+. In addition, bleaching of β-carotene and annatto was observed. Biotransformation experiments verified the alkene cleavage activity towards the aryl alkenes (E)-methyl isoeugenol, α-methylstyrene, and trans-anethole, which was increased almost twofold in the presence of Mn2+. The resultant aldehydes are olfactants used in the fragrance and flavor industry. PsaPOX is the first described DyP with alkene cleavage activity towards aryl alkenes and showed potential as biocatalyst for flavor production.

scholarly journals The amino acid sequence of Pseudomonas fluorescens azurin

1967 ◽  
Vol 104 (3) ◽  
pp. 784-825 ◽  
Author(s):  
RP Ambler ◽  
LH Brown
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Pseudomonas Fluorescens

Protein tertiary structure prediction using hidden Markov model based on lattice

2019 ◽  
Vol 17 (02) ◽  
pp. 1950007
Author(s):  
Farzad Peyravi ◽  
Alimohammad Latif ◽  
Seyed Mohammad Moshtaghioun
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Hidden Markov ◽  
Face Centered Cubic ◽  
Tertiary Structure Prediction ◽  
Cubic Lattices ◽  
Face Centered ◽  
Protein Tertiary Structure Prediction

The prediction of protein structure from its amino acid sequence is one of the most prominent problems in computational biology. The biological function of a protein depends on its tertiary structure which is determined by its amino acid sequence via the process of protein folding. We propose a novel fold recognition method for protein tertiary structure prediction based on a hidden Markov model and 3D coordinates of amino acid residues. The method introduces states based on the basis vectors in Bravais cubic lattices to learn the path of amino acids of the proteins of each fold. Three hidden Markov models are considered based on simple cubic, body-centered cubic (BCC) and face-centered cubic (FCC) lattices. A 10-fold cross validation was performed on a set of 42 fold SCOP dataset. The proposed composite methodology is compared to fold recognition methods which have HMM as base of their algorithms having approaches on only amino acid sequence or secondary structure. The accuracy of proposed model based on face-centered cubic lattices is quite better in comparison with SAM, 3-HMM optimized and Markov chain optimized in overall experiment. The huge data of 3D space help the model to have greater performance in comparison to methods which use only primary structures or only secondary structures.

Synopses from the poster exhibition organized by I. M. Kerr, 1. Interferon: a tertiary structure predicted from amino acid sequences

1982 ◽  
Vol 299 (1094) ◽  
pp. 125-127 ◽  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Functional Studies

Functional studies on interferon would be helped by a three-dimensional structure for the molecule. However, it may be several years before the structure of the protein is determined by X-ray crystallography. We have therefore used available methods for predicting the secondary - and the tertiary - structure of a protein from its amino acid sequence to propose a tertiary model involving the packing of four a-helices. Details of this work have been published elsewhere (Sternberg & Cohen 1982).

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