In-Silico Characterization and Homology Modeling of Catechol 1, 2 dioxygenase Involved in Processing of Catechol - an Intermediate of Aromatic Compound Degradation Pathway

Al-Hakim; Mahmudul Hasan; Rokib Hasan; Md. Hazrat Ali; Muhammad Fazle Rabbee

In-Silico Characterization and Homology Modeling of Catechol 1, 2 dioxygenase Involved in Processing of Catechol – an Intermediate of Aromatic Compound Degradation Pathway

Al-Hakim * §

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Mahmudul Hasan

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Rokib Hasan

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Md. Hazrat Ali

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Muhammad Fazle Rabbee

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§ Shahjalal University of Science and Technology

In-Silico Characterization and Homology Modeling of Catechol 1, 2 dioxygenase Involved in Processing of Catechol – an Intermediate of Aromatic Compound Degradation Pathway

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Abstract

Catechol 1, 2 dioxygenase (EC 1.13.11.1) is an enzyme intended to catalyze the degradation of catechol an intermediate of phenolic compound from ortho-mechanisms of the 3-oxoadipate pathway. Catechol 1, 2 dioxygenase plays a key role in the aerobic degradation of aromatic compounds, because it is the substrate for aromatic ring cleavage enzymes and as such it can be the starting point of many peripheral metabolic pathways. So, catechol 1, 2 dioxygenase is deliberated for a solution of environmental pollution occurred by aromatic compounds. In this study, we have focused on the in-silico characterization and homology modeling of catechol 1, 2 dioxygenase. The in silico analysis was performed by various computational tools and programmes. The physicochemical properties of the selected catechol 1, 2 dioxygenase were analyzed by using ExPASy’sProtParam tool and it was found that the molecular weight (M.Wt) ranges around 35000 Da. Isoelectric Points (pI) exhibits acidic nature and aliphatic index infers that 95% catechol 1, 2 dioxygenaseare stable. The negative value of GRAVY indicates that there will be better interaction with water. Motif analysis of the sequences was conducted by using MEME for predicting probable domain of catechol 1, 2-dioxygenase. Homology modeling of catechol 1, 2 dioxygenase taken from Pseudomonas aeruginosa MH38 (AC NO: CDH71767) was performed by I-TASSER. Various bioinformatics programmes and servers like RAMPAGE, PROCHECK and ERRAT were used for analysis and validation of final 3D structures created through homology modeling.

References

34 Cites in Article

Reference Format

M Hasan,A Hakim,A Iqbal,R Farhana,M Kulsuma,S Sharmin,R Abir (2015). Computational Study and Homology Modeling of Phenol Hydroxylase: Key Enzyme for Phenol Degradation.
M Hasan,Z Joy,H Elius,M Islam (2014). In Silico Characterization and Motif Election of Neurotoxins from Snake Venom.
Lidianne Rocha,Rossana De Aguiar Cordeiro,Rivelino Cavalcante,Ronaldo Do Nascimento,Suzana Martins,Sandra Santaella,Vânia Melo (2007). Isolation and characterization of phenol-degrading yeasts from an oil refinery wastewater in Brazil.
N Ruiz-Ordaz,J Ruiz-Lagunez,J Castanon-Gonzalez (2001). Phenol biodegradation using a repeated batch culture of Candida Tropicalisina multistage bubble column.
D Liu,H Liu,X Gao,D Leak,N Zhou (2005). Arg169 is essential for catalytic activity of 3hydroxybenzoate 6-hydroxylase from Klebsiellapneumoniae M5a1.
J Wu,K Rudy,J Spark (2000). Oxidation of aqueous phenol by ozone and peroxidase.
Z Lazarova,S Boyadzhieva (2004). Treatment of phenol-containing aqueous solutions by membrane-based solvent extraction in coupled ultrafiltration modules.
W Kujawski,A Warszawski,W Ratajczak,T Pore,Capała ¸bski,I Ostrowska (2004). Removal of phenol from wastewater by different separation techniques.
A Hamad,A Aidan,M Fayed,M Mehrvar (2005). Experimental investigation of phenolic wastewater treatment using combined activated carbon and UV processes.
Manuel Carmona,Antonio Lucas,José Valverde,Belén Velasco,Juan Rodríguez (2006). Combined adsorption and ion exchange equilibrium of phenol on Amberlite IRA-420.
M Vidali (2001). Bioremediation. An overview.
R Atlas,R Unterman Bioremediation in: industrial Microbiology & Biotechno.
R Stainer,L Ornston (1973). The β-Ketoadipate Pathway.
S Agarry,A Durojaiye,B Solomon Microbial degradation of phenols: a review.
C Bayly,J Wigmore (1973). Metabolism of phenol and cresols by mutants of Pseudomonas putida.
S Dagley,D Gibson (1965). The bacterial degradation of catechol.
K Watanabe,S Yamamoto,S Hino,S Harayama (1998). Population dynamics of phenol degrading bacteria in activated sludge determined by gyr B-targeted quantitative PCR.
A Kahru,A Maloverjan,H Sillak,L Pollumaa (2002). The toxicity and fate of phenolic pollutants in the contaminated soils associated with the oilshaleindustry.
Christel Hinteregger,Raimund Leitner,Michael Loidl,Andreas Ferschl,Franz Streichsbier (1992). Degradation of phenol and phenolic compounds by Pseudomonas putida EKII.
K Kwon,S Yeom (2009). Optimal microbial adaptation routes for the rapid degradation of high concentration of phenol.
S Seker,H Beyenal,B Salih,A Tomas (1997). Multi-substrate growth kinetics of Pseudomonas putidafor phenol removal.
C Nakai,K Horiike,S Kuramitsu,H Kagamiyama,M Nozaki (1990). Three isozymes of catechol 1,2-dioxygenase (pyrocatechase), alpha alpha, alpha beta, and beta beta, from Pseudomonas arvilla C-1..
C Wang,S You,S Wang,J Sarvanan (2006). Modeling the interaction of Trehalose-6-Phosphate synthase and UDP-glucose bycomputational methods.
T Aldrich,A Chakrabarty (1988). Transcriptional regulation, nucleotide sequence, and localization of the promoter of the catBC operon in Pseudomonas putida.
E Neidle,C Hartnett,L Ornston (1989). Characterization of Acinetobactercalcoaceticuscat M, a repressor gene homologous in sequence to transcriptional activator genes.
K Sivakumar,S Balaji,Gangaradhakrishnan (2007). In silico characterization of antifreeze proteins using computational tools and servers.
Kunchur Guruprasad,B Reddy,Madhusudan Pandit (1990). Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting <i>in vivo</i> stability of a protein from its primary sequence.
J Walker (2005). The Proteomics Protocols Handbook.
Manfred Sippl (1993). Recognition of errors in three‐dimensional structures of proteins.
C1 Colovos,T Yeates (1993). Verification of protein structures: patterns of nonbonded atomic interactions.
R Laskowski,M Macarthur,D Moss,J Thornton (1993). PROCHECK: a program to check the stereochemical quality of protein structures.
S Rogers,R Wells,M Rechsteiner (1986). Amino acid seq-uences common to rapidly degraded proteins: The PEST hypothesis.
E Baker,H Baker,R Kidd (2002). Lactoferrin and transferrin: Functional variations on a common structural framework.
V Colovos,T Yeates (1993). Verification of protein structures: Patterns of non-bonded atomic interactions.

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Funding

No external funding was declared for this work.

Conflict of Interest

The authors declare no conflict of interest.

Ethical Approval

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How to Cite This Article

Al-Hakim, Mahmudul Hasan, Rokib Hasan, Md. Ali, Muhammad Rabbee. 2015. "In-Silico Characterization and Homology Modeling of Catechol 1, 2 dioxygenase Involved in Processing of Catechol – an Intermediate of Aromatic Compound Degradation Pathway". Global Journal of Science Frontier Research, Global Journal of Science Frontier Research - G: Bio-Tech & Genetics GJSFR-G Volume 15 (GJSFR Volume 15 Issue G1).

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GJSFR Volume 15 Issue G1

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Journal Specifications

Crossref Journal DOI 10.17406/GJSFR

Print ISSN 0975-5896

e-ISSN 2249-4626

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GJSFR-G Classification FOR Code: 060102

Submission ReceivedAugust 2, 2015
Peer Review Double Blind
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Accepted September 1, 2015
Published September 14, 2015

Version of record

v1.2

Issue date

October 17, 2015

Language

English

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Article Matrices

Total Score: 152

Country: Bangladesh

Subject: Global Journal of Science Frontier Research

Authors: Al-Hakim, Mahmudul Hasan, Rokib Hasan, Md. Hazrat Ali, Muhammad Fazle Rabbee, Marufatuzzahan, Hanif Mohammad Rejwan, Ziaul Faruque Joy (PhD/Dr. count: 0)

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