MapsiDB: an integrated web database for type I polyketide synthases

Tae, Hongseok; Sohng, Jae Kyung; Park, Kiejung

doi:10.1007/s00449-008-0296-3

Cited by 17 publications

(10 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Polyalanine linkers were built using Coot in order to connect the KS+AT dimer with the DE+KR dimer, the DE+KR dimer with the ACP domains, and the ACP domains with the downstream KS+AT dimer 35 . Linker lengths were determined from sequence alignments of appropriate linkers obtained from MAPSI (Supplementary Figure 3) 50,27 . Measurements were made between residues known to be structured; the linker spanning KS+AT and DE was measured between the YWL motif and 5 residues prior to the first conserved DE tryptophan; the linker spanning KR and ACP was measured between 7 residues after a highly conserved proline and helix 0 26 ; the linker spanning ACP and KS was measured between the last highly conserved ACP glycine and the first highly conserved KS proline.…”

Section: Methodsmentioning

confidence: 99%

The Missing Linker: A Dimerization Motif Located within Polyketide Synthase Modules

et al. 2013

View full text Add to dashboard Cite

The dimerization of multimodular polyketide synthases is essential for their function. Motifs that supplement the contacts made by dimeric polyketide synthase enzymes have previously been characterized outside the boundaries of modules, at the N- and C-terminal ends of polyketide synthase subunits. Here we describe a heretofore-uncharacterized dimerization motif located within modules. The dimeric state of this dimerization element was elucidated through the 2.6 Å-resolution crystal structure of a fragment containing a dimerization element and a ketoreductase. The solution structure of a standalone dimerization element was revealed by nuclear magnetic resonance spectroscopy to be consistent with that of the crystal structure, and its dimerization constant was measured through analytical ultracentrifugation to be ~20 μM. The dimer buries ~990 Å2 at its interface, and its C-terminal helices rigidly connect to ketoreductase domains to constrain their locations within a module. These structural restraints permitted the construction of a common type of polyketide synthase module.

show abstract

Section: Methodsmentioning

confidence: 99%

The Missing Linker: A Dimerization Motif Located within Polyketide Synthase Modules

et al. 2013

View full text Add to dashboard Cite

show abstract

“…Each catalytic domain for modular type I PKSs is used only once during the biosynthetic process. A type I iterative PKS is usually composed of one module, which iteratively performs a set of activities, used in condensation and chain elongation steps [4,5]. Up to now, many of the macrolides synthesized by modular (type I) PKS have been described to date [6].…”

Section: Introduction *mentioning

confidence: 99%

Diversity analysis of type I ketosynthase in rhizosphere soil of cucumber

Zhao

Gao

Shao

et al. 2011

J. Basic Microbiol.

View full text Add to dashboard Cite

Fusarium wilt [Fusarium oxysporum (Sch1.) f.sp. cucumerinum Owen.] is a major soil-borne disease of cucumber worldwide, and can cause huge yield losses. Biological control of Fusarium wilt of cucumber has received considerable attention. Many bacteria, particularly actinomycetes, are known to produce secondary metabolites synthesized by Polyketide synthases (PKSs) with a diverse range of biological activities. Ketosynthase (KS) gene diversity was analyzed in samples which were collected from rhizosphere soil of both diseased cucumber and healthy cucumber in Dalian, China. The phylogenetic analysis amino acid (AA) sequences indicated that the KS genes in the rhizosphere soil samples were clustered into diverse seven clades, including Sorangium cellulosum, Anabaena variabilis, Nostoc punctiforme, Xanthobacter autotrophicus, Streptomyces, myxobacteria and uncultured bacteria. Among seven major clades in the phylogenetic tree, two clades were peculiar to rhizosphere soil of diseased cucumber and one was peculiar to healthy cucumber. Among the 182 cloned KS genes, 147 KS genes were clustered with the uncultured bacteria group. Most of the KS genes showed about 80% similarity at the AA level to sequences known in GenBank. These results revealed the great diversity and novelty of KS genes in rhizosphere soil of cucumber.

show abstract

“…Aspergillus genome was searched for putative PKS sequences by subjecting the protein sequence of KS domain of PKSP (XP_756095.1) of A. fumigatus Af293 as a query into BLASTp. Domains in PKS were searched by subjecting each putative amino acid sequence to online tools SEARCHPKS, 20 MapsiDB, 21 and CDD (NCBI). A total of 190 Aspergilli PKS sequences were retrieved and analyzed in this study.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic and Structural Analysis of Polyketide Synthases in Aspergilli

Bhetariya

Prajapati

Bhaduri

et al. 2016

Evol Bioinform Online

View full text Add to dashboard Cite

Polyketide synthases (PKSs) of Aspergillus species are multidomain and multifunctional megaenzymes that play an important role in the synthesis of diverse polyketide compounds. Putative PKS protein sequences from Aspergillus species representing medically, agriculturally, and industrially important Aspergillus species were chosen and screened for in silico studies. Six candidate Aspergillus species, Aspergillus fumigatus Af293, Aspergillus flavus NRRL3357, Aspergillus niger CBS 513.88, Aspergillus terreus NIH2624, Aspergillus oryzae RIB40, and Aspergillus clavatus NRRL1, were selected to study the PKS phylogeny. Full-length PKS proteins and only ketosynthase (KS) domain sequence were retrieved for independent phylogenetic analysis from the aforementioned species, and phylogenetic analysis was performed with characterized fungal PKS. This resulted into grouping of Aspergilli PKSs into nonreducing (NR), partially reducing (PR), and highly reducing (HR) PKS enzymes. Eight distinct clades with unique domain arrangements were classified based on homology with functionally characterized PKS enzymes. Conserved motif signatures corresponding to each type of PKS were observed. Three proteins from Protein Data Bank corresponding to NR, PR, and HR type of PKS (XP_002384329.1, XP_753141.2, and XP_001402408.2, respectively) were selected for mapping of conserved motifs on three-dimensional structures of KS domain. Structural variations were found at the active sites on modeled NR, PR, and HR enzymes of Aspergillus. It was observed that the number of iteration cycles was dependent on the size of the cavity in the active site of the PKS enzyme correlating with a type with reducing or NR products, such as pigment, 6MSA, and lovastatin. The current study reports the grouping and classification of PKS proteins of Aspergilli for possible exploration of novel polyketides based on sequence homology; this information can be useful for selection of PKS for polyketide exploration and specific detection of Aspergilli.

show abstract

MapsiDB: an integrated web database for type I polyketide synthases

Cited by 17 publications

References 26 publications

The Missing Linker: A Dimerization Motif Located within Polyketide Synthase Modules

The Missing Linker: A Dimerization Motif Located within Polyketide Synthase Modules

Diversity analysis of type I ketosynthase in rhizosphere soil of cucumber

Phylogenetic and Structural Analysis of Polyketide Synthases in Aspergilli

Contact Info

Product

Resources

About