Three Dimensional Structural Modelling of Lipase Encoding Gene from Soil Bacterium &lt;i&gt;Alcaligenes&lt;/i&gt; sp. JG3 Using Automated Protein Homology Analysis

Nataningtyas, Dilin Rahayu; Raharjo, Tri Joko; Astuti, Endang

doi:10.22146/ijc.34152

Cited by 3 publications

(5 citation statements)

References 29 publications

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“…In silico approximation was used to analyze the homology, structure, and function of Lip.JG3 [15]. Alignment of multiple lipase sequences was performed using MUSCLE (https://www.ebi.ac.uk/Tools/msa/ muscle/), the distribution of secondary structure of Lip.JG3 was carried out using PSIPRED server (http://bioinf.…”

Section: Analysis Of Lipase Protein Structure and Functionmentioning

confidence: 99%

“…Many suggestions have been proposed to solve the mechanism of ABC protein to hydrolyze the appropriate substrate. The Walker-B motif, specifically the glutamic acid residue is predicted as the active site as it directly binds into the phosphodiester bond resulting hydrolysis reaction [15]. Residues of T 43 , Q 88 , D1 64 , and E 165 from Lip.JG3 amino acid sequence was predicted to have the ability to bind Mg 2+ , as well as from another ABC Transporter protein.…”

Section: Active Site Of Lipase Jg3mentioning

confidence: 99%

“…An attempt to understand the Alcaligenes sp. JG3's lipase (defined as Lip.JG3) have been carried out including investigation of its characteristic and activity as a catalyst, mapping its nucleotide and amino acid sequences and also cloning of the gene [11,[15][16][17]. In this report, overexpression of Lip.JG3 has been carried out successfully.…”

Section: ■ Introductionmentioning

confidence: 99%

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Overexpression of Lipase Gene from <i>Alcaligenes</i> sp. JG3 and its Activity toward Hydrolysis Reaction

2019

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Bacterial lipase holds an important role as a new source for many industrial catalysts. The investigation and understanding of the lipase-encoding gene become apparent as the key step for generating high-quality lipase as biocatalyst for many chemical reactions. In this study, bacterial lipase from Alcaligenes sp. JG3 was produced via overexpression gene method. This specific lipase was successfully overexpressed using pQE-30 vector and E. coli M15[pREP4] as host, producing His-tagged protein sized 46 kDa and was able to hydrolyze triacylglycerol from olive oil with the calculated unit activity and specific activity of 0.012 U and 1.175 U/mg respectively. The in silico investigation towards lipase JG3 revealed that it was categorized as ABC transporter protein as opposed to the conventional hydrolase family. Lastly, amino acid sequences SGSGKTT from lipase JG3 was highly conserved sequences and was predicted as the ATP-binding site but the catalytic triad of serine, histidine, and aspartate has not been solved yet.

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Section: Analysis Of Lipase Protein Structure and Functionmentioning

confidence: 99%

Section: Active Site Of Lipase Jg3mentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

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Overexpression of Lipase Gene from <i>Alcaligenes</i> sp. JG3 and its Activity toward Hydrolysis Reaction

2019

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“…Alcaligenes sp. are also an important source for some enzyme research (Bhatia et al, 2014;Nataningtyas et al, 2019). The use of Alcaligenes sp.…”

Section: Introductionmentioning

confidence: 99%

Effect of Alcaligenes sp. on corrosion behavior of X65 steel in simulated offshore oilfield-produced water

Shi

Wang

2023

Front. Microbiol.

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In this paper, the effect of Alcaligenes sp. on the corrosion process of X65 steel was investigated by using non-targeted metabolomics techniques for comprehensive characterization of metabolites, combined with surface analysis techniques and electrochemical testing. The results showed that the organic acids produced by Alcaligenes sp. accelerated the corrosion process of X65 steel in the early stage, and the presence of Alcaligenes sp. promoted the deposition of stable corrosion products and minerals in the middle and late stages. In addition, proteoglycans and corrosion inhibiting substances were enriched on the metal surface, which enhanced the stability of the film. The combined effect of multiple factors makes the mixed film of biofilm and corrosion products more dense and complete, which effectively inhibits the corrosion of X65 steel.

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“…Information regarding genes that encode the protease of L. mesenteroides K7 is vital for protease structural investigation. Gene characterization of bacterial such as L. mesenteroides K7 can be carried out using PCR gene amplification followed sequencing of the PCR product and further analysis of the sequence such as homology analysis as well as modeling of the deductive protein sequence encoded by gene (Biasini et al 2014;Yan and Fong 2018;Nataningtyas et al 2019). The protease-coding gene has a diverse sequence between organisms, which can be traced in vitro through polymerase chain reaction (PCR) technique using primers that are designed based on known gene sequences from other species that have a close taxonomy relationship.…”

Section: Introductionmentioning

confidence: 99%

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

2020

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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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Three Dimensional Structural Modelling of Lipase Encoding Gene from Soil Bacterium <i>Alcaligenes</i> sp. JG3 Using Automated Protein Homology Analysis

Cited by 3 publications

References 29 publications

Overexpression of Lipase Gene from <i>Alcaligenes</i> sp. JG3 and its Activity toward Hydrolysis Reaction

Overexpression of Lipase Gene from <i>Alcaligenes</i> sp. JG3 and its Activity toward Hydrolysis Reaction

Effect of Alcaligenes sp. on corrosion behavior of X65 steel in simulated offshore oilfield-produced water

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

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