Cloning, sequence analysis and three-dimensional structure prediction of DNA pol I from thermophilic Geobacillus sp. MKK isolated from an Iranian hot spring

Molecular phylogenetic analysis of a novel thermophilic eubacterium isolated from an Iranian hot spring using 16S rDNA sequence showed that the new isolate belongs to genera Geobacillus. DNA pol I gene from this isolate was amplified, cloned, sequenced, and the three-dimensional (3D) structure of de...

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Bibliographic Details
Published in:	Applied biochemistry and biotechnology Vol. 142; no. 2; pp. 200 - 208
Main Authors:	KHALAJ-KONDORI, Mohammad, SADEGHIZADEH, Majid, KHAJEH, Khosro, NADERI-MANESH, Hossein, ALI MOHAMMAD AHADI, EMAMZADEH, Abdorahman
Format:	Journal Article
Language:	English
Published:	Heidelberg Springer 01-08-2007 Springer Nature B.V
Subjects:	Amino Acid Sequence Amino acids Bacillaceae - classification Bacillaceae - enzymology Bacillus stearothermophilus Bacteria Binding sites Biological and medical sciences Biotechnology Cloning Cloning, Molecular Deoxyribonucleic acid DNA DNA Polymerase I - chemistry DNA Polymerase I - genetics DNA, Ribosomal - chemistry Enzymes Eubacterium Exonucleases - chemistry Fundamental and applied biological sciences. Psychology Geobacillus Hot springs Hot Springs - microbiology Iran Models, Molecular Molecular Sequence Data Phylogeny Protein Structure, Tertiary Sequence Analysis Iran Thermostable DNA pol I Three dimensional structure Gsm pol I DNA Cloning Prediction Thermophily Hot source Phylogeny Thermal stability 3D structure prediction Molecular phylogenetic
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Summary:	Molecular phylogenetic analysis of a novel thermophilic eubacterium isolated from an Iranian hot spring using 16S rDNA sequence showed that the new isolate belongs to genera Geobacillus. DNA pol I gene from this isolate was amplified, cloned, sequenced, and the three-dimensional (3D) structure of deduced amino acid sequence was predicted. Sequence analysis revealed the gene is 2,631 bp long, encodes a protein of 876 amino acids with a calculated molecular mass of 99 kDa, and belongs to family A DNA polymerases. Comparison of 3'-5'exonuclease domain of Klenow fragment (KF) with corresponding region of newly identified DNA pol I (MF), the large fragment of Bacillus stearothermophilus DNA pol I (BF) and Klentaq1, revealed not only deletions in three regions compared to KF, but that three of the four critical metal-binding residues in KF (Asp355, Glu357, Asp424, and Asp501) are altered in MF as well. Predicted 3D structure and sequence alignments between MF and BF showed that all critical residues in the polymerase active site are conserved.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0273-2289 1559-0291
DOI:	10.1007/s12010-007-0010-y