Sequences Analysis of a Gene Encoding Extracellular Xylanase in Streptomyces costaricanus 45I-3

Abstract

Streptomyces costaricanus 45I-3 is a bacterial strain belongs to actinomycetes group isolated from peat soil. The bacterium is known to produce extracellular xylanase. The aims of this study were to analyze DNA sequence and sub-clone gene involved in the synthesis of extracellular xylanase. Complete DNA sequence predicted to encode xylanase genes was isolated from bacterial genome using Inverse Polymerase Chain Reaction (I-PCR). Total DNA sequence of 1664 bp in size obtained from I-PCR consisted of two open reading frames (ORF) in opposite direction. ORF1 was 1029 bp and ORF2 (partial sequence) was 309 bp. Analysis sequence using BlastX indicated that ORF1 was homologous with xylanase bacterium enrichment culture clone Xyl8B8 (GenBank accession No. AFH35005.1), i.e. 95% in identity and 99% in similarity. In addition, ORF2 was homologous with glyoxalase bacterium enrichment culture clone Xyl8B8 (GenBank accession No. AFH35007.1), i.e. 95% in identity and 98% in similarity. Analysis of amino acid sequence revealed that ORF1 consisted of 2 domains, i.e. glyco-hydrolase 11 (GH11) and Carbohydrate Binding Type 2 (CBM2). Active site was found at 130th amino acid on GH11 domain. Visualization of 3-dimension structure showed that 1029 bp fragment is of 19 areas.

Keywords

• Streptomyces costaricanus 45I-3
• xylanase extracellular
• Inverse-PCR