TITLE

Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4-55 PHA synthase and an insight into its catalytic mechanism

AUTHOR(S)
Wahab, Habibah A.; Khairudin, Nurul Bahiyah Ahmad; Samian, Mohd Razip; Najimudin, Nazalan
PUB. DATE
January 2006
SOURCE
BMC Structural Biology;2006, Vol. 6, p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Polyhydroxyalkanoates (PHA), are biodegradable polyesters derived from many microorganisms such as the pseudomonads. These polyesters are in great demand especially in the packaging industries, the medical line as well as the paint industries. The enzyme responsible in catalyzing the formation of PHA is PHA synthase. Due to the limited structural information, its functional properties including catalysis are lacking. Therefore, this study seeks to investigate the structural properties as well as its catalytic mechanism by predicting the three-dimensional (3D) model of the Type II Pseudomonas sp. USM 4-55 PHA synthase 1 (PhaC1P.sp USM 4-55). Results: Sequence analysis demonstrated that PhaC1P.sp USM 4-55 lacked similarity with all known structures in databases. PSI-BLAST and HMM Superfamily analyses demonstrated that this enzyme belongs to the alpha/beta hydrolase fold family. Threading approach revealed that the most suitable template to use was the human gastric lipase (PDB ID: 1HLG). The superimposition of the predicted PhaC1P.sp USM 4-55 model with 1HLG covering 86.2% of the backbone atoms showed an RMSD of 1.15 Ã…. The catalytic residues comprising of Cys296, Asp451 and His479 were found to be conserved and located adjacent to each other. In addition to this, an extension to the catalytic mechanism was also proposed whereby two tetrahedral intermediates were believed to form during the PHA biosynthesis. These transition state intermediates were further postulated to be stabilized by the formation of oxyanion holes. Based on the sequence analysis and the deduced model, Ser297 was postulated to contribute to the formation of the oxyanion hole. Conclusion: The 3D model of the core region of PhaC1P.sp USM 4-55 from residue 267 to residue 484 was developed using computational techniques and the locations of the catalytic residues were identified. Results from this study for the first time highlighted Ser297 potentially playing an important role in the enzyme's catalytic mechanism.
ACCESSION #
29323582

 

Related Articles

  • Structural Insights into the UbiD Protein Family from the Crystal Structure of PA0254 from Pseudomonas aeruginosa Jacewicz, Agata; Izumi, Atsushi; Brunner, Katharina; Schnell, Robert; Schneider, Gunter // PLoS ONE;May2013, Vol. 8 Issue 5, p1 

    The 3-polyprenyl-4-hydroxybenzoate decarboxylase (UbiD) catalyzes the conversion of 3-polyprenyl-4-hydroxybenzoate to 2-polyprenylphenol in the biosynthesis of ubiquinone. Pseudomonas aeruginosa contains two genes (PA0254 and PA5237) that are related in sequence to putative UbiD enzymes. A...

  • The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4. Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J.; Glick, Bernard R. // PLoS ONE;Mar2013, Vol. 8 Issue 3, p1 

    The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt,...

  • Cloning and Nucleotide Sequence Analysis of xyIE Gene Responsible for meta-Cleavage of 4-Chlorocatechol from Pseudomonas sp. S-47. Sang-Jin Noh; Youngsoo Kim; Kyung-Hee Min; Karegoudar, T. B.; Chi-Kyung Kim // Molecules & Cells (Springer Science & Business Media B.V.);2000, Vol. 10 Issue 4, p475 

    Presents a study which focused on cloning and nucleotide sequence analysis of xylE gene responsible for meta-cleavage of 4-chlorocatechol from pseudomonas sp. S-47. Materials and methods; Results; Discussion.

  • Acetylating Tryptic Peptides Enhances b Ion Intensity in MALDI TOF/TOF: Implications in Peptide Sequencing and Identification of Proteins in an Antarctic Bacterium Pseudomonas Syringae. Kulkarni, Heramb M.; Ramesh, V.; Srinivas, R.; Jagannadham, M. V. // Proteomics Insights;2010, Issue 3, p1 

    Several approaches have been described to identify proteins from MALDI MS/MS mass spectra. The sequence of tryptic peptides is determined by database searching or by de novo sequencing. Different algorithms are available to determine peptide sequence using mass spectra. False discovery of...

  • Physiological and genetic characterization of fluorescent Pseudomonas associated with Cantharellus cibarius. Rangel-Castro, J Ignacio; Levenfors, Jolanta J; Danell, Eric // Canadian Journal of Microbiology;Aug2002, Vol. 48 Issue 8, p739 

    Fluorescent Pseudomonas spp. isolated from fruiting bodies (FB) of Cantharellus cibarius were characterized physiologically and genetically and were compared with fluorescent Pseudomonas from forest soil and with sequences from the GenBank database. Pseudomonas spp. from FB differed...

  • Cystovirus. Bamford, Dennis H. // Springer Index of Viruses;2002, p290 

    The article presents information on cystovirus, a genus of the family Cystoviridae. Its virion, genome and replication strategy are mentioned. The virus was discovered in 1973. Another member of the family is pseudomonas phage. The nucleotide sequences, proteins and biology of the virus species...

  • Identification of signature and primers specific to genus Pseudomonas using mismatched patterns of 16S rDNA sequences. Purohit, H. J.; Raje, D. V.; Kapley, A. // BMC Bioinformatics;2003, Vol. 4, p1 

    Background: Pseudomonas, a soil bacterium, has been observed as a dominant genus that survives in different habitats with wide hostile conditions. We had a basic assumption that the species level variation in 16S rDNA sequences of a bacterial genus is mainly due to substitutions rather than...

  • Characterization of a New Cold-adapted Lipase from Pseudomonas sp. TK-3. Tanaka, Daisuke; Yoneda, Satoru; Yamashiro, Yoko; Sakatoku, Akihiro; Kayashima, Takuro; Yamakawa, Kasumi; Nakamura, Shogo // Applied Biochemistry & Biotechnology;Sep2012, Vol. 168 Issue 2, p327 

    A psychrotrophic Pseudomonas sp. TK-3 was isolated from dirty and cool stream water in Toyama, Japan from which we cloned and characterized the bacterial lipase LipTK-3. The sequenced DNA fragment contains an open reading frame of 1,428 bp that encoded a protein of 476 amino acids with an...

  • Isolation and characterization of a nicotine-degrading bacterium CW6 strain. ZHAI Guifa; CHEN Suhui; LI Han; WANG Yingyue; YANG Xiaotong; WANG Xiaoli; GUO Li; LI Xiaohua // Journal of Huazhong Normal University;Oct2013, Vol. 52 Issue 5, p676 

    A nicotine-degrading bacterium, strainCW6, was isolated from the tobacco fieldsoil, using nicotine as the sole source of carbon. Based on standard morphologica1, physiological properties and 16Sr RNA gene sequence, it was identified as Pseudomonas sp. With in itial nicotine concentration of...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics