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1. Kim  BJ, Kim  CJ, Chun  J, Koh  YH, Lee  SH, Hyun  JW, Cha  CY, Kook  YH,     ( 2004 )

Phylogenetic analysis of the genera Streptomyces and Kitasatospora based on partial RNA polymerase beta-subunit gene (rpoB) sequences.

International journal of systematic and evolutionary microbiology 54 (Pt 2)
PMID : 15023980  :   DOI  :   10.1099/ijs.0.02941-0    
Abstract >>
The RNA polymerase beta-subunit genes (rpoB) of 67 Streptomyces strains, representing 57 species, five Kitasatospora strains and Micromonospora echinospora KCTC 9549 were partially sequenced using a pair of rpoB PCR primers. Among the streptomycetes, 99.7-100 % similarity within the same species and 90.2-99.3 % similarity at the interspecific level were observed by analysis of the determined rpoB sequences. The topology of the phylogenetic tree based on rpoB sequences was similar to that of 16S rDNA. The five Kitasatospora strains formed a stable monophyletic clade and a sister group to the clade comprising all Streptomyces species. Although there were several discrepancies in the details, considerable agreement was found between the results of rpoB analysis and those of numerical phenetic classification. This study demonstrates that analysis of rpoB can be used as an alternative genetic method in parallel to conventional taxonomic methods, including numerical phenetic and 16S rDNA analyses, for the phylogenetic analyses of the genera Streptomyces and Kitasatospora.
KeywordMeSH Terms
2. Zhang  W, Ntai  I, Bolla  ML, Malcolmson  SJ, Kahne  D, Kelleher  NL, Walsh  CT,     ( 2011 )

Nine enzymes are required for assembly of the pacidamycin group of peptidyl nucleoside antibiotics.

Journal of the American Chemical Society 133 (14)
PMID : 21417270  :   DOI  :   10.1021/ja2011109     PMC  :   PMC3071879    
Abstract >>
Pacidamycins are a family of uridyl peptide antibiotics that inhibit the translocase MraY, an essential enzyme in bacterial cell wall biosynthesis that to date has not been clinically targeted. The pacidamycin structural skeleton contains a doubly inverted peptidyl chain with a �]-peptide and a ureido linkage as well as a 3'-deoxyuridine nucleoside attached to DABA(3) of the peptidyl chain via an enamide linkage. Although the biosynthetic gene cluster for pacidamycins was identified recently, the assembly line of this group of peptidyl nucleoside antibiotics remained poorly understood because of the highly dissociated nature of the encoded nonribosomal peptide synthetase (NRPS) domains and modules. This work has identified a minimum set of enzymes needed for generation of the pacidamycin scaffold from amino acid and nucleoside monomers, highlighting a freestanding thiolation (T) domain (PacH) as a key carrier component in the peptidyl chain assembly as well as a freestanding condensation (C) domain (PacI) catalyzing the release of the assembled peptide by a nucleoside moiety. On the basis of the substrate promiscuity of this enzymatic assembly line, several pacidamycin analogues were produced using in vitro total biosynthesis.
KeywordMeSH Terms
3. Zhang  W, Ostash  B, Walsh  CT,     ( 2010 )

Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics.

Proceedings of the National Academy of Sciences of the United States of America 107 (39)
PMID : 20826445  :   DOI  :   10.1073/pnas.1011557107     PMC  :   PMC2947877    
Abstract >>
Pacidamycins are a family of uridyl tetra/pentapeptide antibiotics that act on the translocase MraY to block bacterial cell wall assembly. To elucidate the biosynthetic logic of pacidamcyins, a putative gene cluster was identified by 454 shotgun genome sequencing of the producer Streptomyces coeruleorubidus NRRL 18370. The 31-kb gene cluster encodes 22 proteins (PacA-V), including highly dissociated nonribosomal peptide synthetase (NRPS) modules and a variety of tailoring enzymes. Gene deletions confirmed that two NRPSs, PacP and PacO, are required for the biosynthesis of pacidamycins. Heterologous expression and in vitro assays of PacL, PacO, and PacP established reversible formation of m-Tyr-AMP, l-Ala-AMP, and diaminopropionyl-AMP, respectively, consistent with the amino acids found in pacidamycin scaffolds. The unusual Ala(4)-Phe(5) dipeptidyl ureido linkage was formed during in vitro assays containing purified PacL, PacJ, PacN, and PacO. Both the genetic and enzymatic studies validate identification of the biosynthetic genes for this subclass of uridyl peptide antibiotics and provide the basis for future mechanistic study of their biosynthesis.
KeywordMeSH Terms
Multigene Family
4. Everest  GJ, Cook  AE, Kirby  BM, Meyers  PR,     ( 2011 )

Evaluation of the use of recN sequence analysis in the phylogeny of the genus Amycolatopsis.

Antonie van Leeuwenhoek 100 (4)
PMID : 21671192  :   DOI  :   10.1007/s10482-011-9604-z    
Abstract >>
Partial recN gene sequences (>1 kb) were obtained from 35 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of recN sequence analysis as an alternative to DNA-DNA hybridization (DDH) for distinguishing closely related species was also assessed. The recN based phylogeny mostly confirmed the conventional 16S rRNA and gyrB gene-based phylogenies and thus provides further support for these phylogenetic groupings. As is the case for the gyrB gene, pairwise recN sequence similarities cannot be used to predict the DNA relatedness between type strains but the recN genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the genus Amycolatopsis. A recN genetic distance of >0.04 between two Amycolatopsis strains is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization of the unknown strain is worth undertaking).
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5. Zhang  W, Ames  BD, Walsh  CT,     ( 2011 )

Identification of phenylalanine 3-hydroxylase for meta-tyrosine biosynthesis.

Biochemistry 50 (24)
PMID : 21615132  :   DOI  :   10.1021/bi200733c     PMC  :   PMC3115494    
Abstract >>
Phenylalanine hydroxylase (PheH) is an iron(II)-dependent enzyme that catalyzes the hydroxylation of aromatic amino acid l-phenylalanine (L-Phe) to l-tyrosine (L-Tyr). The enzymatic modification has been demonstrated to be highly regiospecific, forming proteinogenic para-Tyr (p-Tyr) exclusively. Here we biochemically characterized the first example of a phenylalanine 3-hydroxylase (Phe3H) that catalyzes the synthesis of meta-Tyr (m-Tyr) from Phe. Subsequent mutagenesis studies revealed that two residues in the active site of Phe3H (Cys187 and Thr202) contribute to C-3 rather than C-4 hydroxylation of the phenyl ring. This work sets the stage for the mechanistic and structural study of regiospecific control of the substrate hydroxylation by PheH.
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6. Harris  NC, Born  DA, Cai  W, Huang  Y, Martin  J, Khalaf  R, Drennan  CL, Zhang  W,     ( 2018 )

Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase.

Angewandte Chemie (International ed. in English) 57 (31)
PMID : 29906336  :   DOI  :   10.1002/anie.201804307     PMC  :   PMC6191297    
Abstract >>
The electron-rich isonitrile is an important functionality in bioactive natural products, but its biosynthesis has been restricted to the IsnA family of isonitrile synthases. We herein provide the first structural and biochemical evidence of an alternative mechanism for isonitrile formation. ScoE, a putative non-heme iron(II)-dependent enzyme from Streptomyces coeruleorubidus, was shown to catalyze the conversion of (R)-3-((carboxymethyl)amino)butanoic acid to (R)-3-isocyanobutanoic acid through an oxidative decarboxylation mechanism. This work further provides a revised scheme for the biosynthesis of a unique class of isonitrile lipopeptides, of which several members are critical for the virulence of pathogenic mycobacteria.
KeywordMeSH Terms
acyl-acyl carrier protein ligase
protein structures
7. Michailidou  F, Chung  CW, Brown  MJB, Bent  AF, Naismith  JH, Leavens  WJ, Lynn  SM, Sharma  SV, Goss  RJM,     ( 2017 )

Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins.

Angewandte Chemie (International ed. in English) 56 (41)
PMID : 28786545  :   DOI  :   10.1002/anie.201705639     PMC  :   PMC5656905    
Abstract >>
The uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3'-deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine-5'-aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3'-deoxy pacidamycin moiety with the synthetic anti-retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.
KeywordMeSH Terms
structural biology

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