scholarly journals Characterization of a novel lipase from Pseudomonas aeruginosa

2019 ◽  
Vol 18 (1) ◽  
pp. 44-51
Author(s):  
Nodir Sh. Berdiev ◽  
Jamolitdin F. Ziyavitdinov ◽  
Akmal M. Asrorov ◽  
Shukhratjon S. Olimjonov ◽  
Shavkat I. Salikhov
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Enzymatic Digestion ◽  
Dimensional Structure ◽  
Fuel Oils ◽  
Potential Alternative ◽  
Lid Domain

Abstract Lipases cleaving oils into fatty acids and glycerol are of great interest for the use in increasing the efficiency of fuels. In this work, a novel lipase from Pseudomonas aeruginosa, P. aeruginosa A12, was isolated by ion-exchange and hydrophobic chromatography. The purity of lipase was shown by electrophoresis and its molecular weight was estimated to be ~ 31.6 kDa. The whole amino acid sequence was analyzed by an LC-MS/MS method. Temperature- and pH-dependent optimum of the enzyme compiled 30 °C and 7.5, respectively. The obtained enzyme exhibited 79 % similarity of amino acid sequence to a lipase isolated from the same strain of P. aeruginosa. Thus, the novel lipase was determined to belong to I.1 subfamily of bacterial true lipases. Three dimensional structure of the isolated lipase isoform was modeled based on obtained sequences. Amino acids forming the catalytic domain were shown in the model. Lid domain is suggested to be in the open conformation. These results provide a potential alternative for enzymatic digestion of fuel oils and serve for the development of fundamental knowledge of lipase activity.

scholarly journals Amino acid sequence and three-dimensional structure of the Tn-specific isolectin B4 fromVicia villosa

FEBS Letters ◽  
1997 ◽  
Vol 412 (1) ◽  
pp. 190-196 ◽  
Author(s):  
Eduardo Osinaga ◽  
Diana Tello ◽  
Carlos Batthyany ◽  
Mario Bianchet ◽  
Gisele Tavares ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Isolectin B4

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).

scholarly journals Amino-acid sequence and predicted three-dimensional structure of pea seed (Pisum sativum) ferritin

1992 ◽  
Vol 288 (3) ◽  
pp. 931-939 ◽  
Author(s):  
S Lobreaux ◽  
S J Yewdall ◽  
J F Briat ◽  
P M Harrison
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Three Dimensional ◽  
Transit Peptide ◽  
Amino Acid Identity ◽  
Dimensional Structure ◽  
Three Dimensional Model ◽  
Iron Storage ◽  
Liver Ferritin ◽  
Pea Seed

The iron storage protein, ferritin, is widely distributed in the living kingdom. Here the complete cDNA and derived amino-acid sequence of pea seed ferritin are described, together with its predicted secondary structure, namely a four-helix-bundle fold similar to those of mammalian ferritins, with a fifth short helix at the C-terminus. An N-terminal extension of 71 residues contains a transit peptide (first 47 residues) responsible for plastid targetting as in other plant ferritins, and this is cleaved before assembly. The second part of the extension (24 residues) belongs to the mature subunit; it is cleaved during germination. The amino-acid sequence of pea seed ferritin is aligned with those of other ferritins (49% amino-acid identity with H-chains and 40% with L-chains of human liver ferritin in the aligned region). A three-dimensional model has been constructed by fitting the aligned sequence to the coordinates of human H-chains, with appropriate modifications. A folded conformation with an 11-residue helix is predicted for the N-terminal extension. As in mammalian ferritins, 24 subunits assemble into a hollow shell. In pea seed ferritin, its N-terminal extension is exposed on the outside surface of the shell. Within each pea subunit is a ferroxidase centre resembling those of human ferritin H-chains except for a replacement of Glu-62 by His. The channel at the 4-fold-symmetry axes defined by E-helices, is predicted to be hydrophilic in plant ferritins, whereas it is hydrophobic in mammalian ferritins.

scholarly journals Three-dimensional structure modeling of a protease from lactic acid bacteria Leuconostoc mesenteroides K7 using automated protein homology analysis

2020 ◽  
Vol 21 (7) ◽  
Author(s):  
Habibi HIdayat ◽  
Winarto Haryadi ◽  
TRI JOKO RAHARJO
Keyword(s):  
Lactic Acid ◽  
Amino Acid ◽  
Lactic Acid Bacteria ◽  
Amino Acid Sequence ◽  
Leuconostoc Mesenteroides ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structure Modeling ◽  
Protein Homology ◽  
Pcr Product

Abstract. Hidayat H, Haryadi W, Raharjo TJ. 2020. Three-dimensional structure modeling of a protease from lactic acid bacteria Leuconostoc mesenteroides K7 using automated protein homology analysis. Biodiversitas 21: 3156-3162. This study aimed to characterize the protease encoding gene of Leuconostoc mesenteroides K7 isolated from Kelengkeng (Dimocarpus longan) fruit as well as to predict the structure of the protein using in silico approach. Gene characterization was performed using PCR employs primers designed based on protease gene of other Leuconostoc species, followed by cloning and sequencing of the PCR product. Protein structural modeling was targeted to the deduced amino acid sequence of the gene employ multiple sequence alignment and SWISS-Model online software.  As a result, the sequence of the PCR product contains an open reading frame with a size of 1,140 bp, which can be translated into 379 amino acids. The amino acid sequence shares 98.60% identity with protease from Leuconostoc suionicum (AP017935.1). Three conserved sequences of QTDA, INPGNSGGPL, and FAIP are known as the signature from the Serine endoprotease DegS family are detected.  The three-dimensional modeling structure application shows that the protein share similarity of 37.62% to Protease Do-like I chloroplastic that belong to serine protease.

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