title: Cloning, sequence analysis and three-dimensional structure prediction of DNA pol I from thermophilic Geobacillus sp. MKK isolated from an Iranian hot spring.
abstract: 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.
authors.affiliation: Department of Biology, Faculty of Basic Sciences, Tarbiat Modares University, Tehran, Iran.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Khalaj-Kondori
authors.forename: Majid
authors.initials: M
authors.lastname: Sadeghizadeh
authors.forename: Khosro
authors.initials: K
authors.lastname: Khajeh
authors.forename: Hossein
authors.initials: H
authors.lastname: Naderi-Manesh
authors.forename: Ali Mohammad
authors.initials: AM
authors.lastname: Ahadi
authors.forename: Abdorahman
authors.initials: A
authors.lastname: Emamzadeh
mesh_terms: D000595:Amino Acid Sequence; D001406:Bacillaceae / Q000145:classification / Q000201:enzymology*; D003001:Cloning, Molecular; D004256:DNA Polymerase I / Q000737:chemistry* / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry; D005092:Exonucleases / Q000737:chemistry; D045482:Hot Springs / Q000382:microbiology*; D007492:Iran; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D017421:Sequence Analysis
chemical_list: D004275:DNA, Ribosomal; D004256:DNA Polymerase I; D005092:Exonucleases