Thermostable alanine racemase from Bacillus stearothermophilus: DNA and protein sequence determination and secondary structure prediction

Katsuyuki Tanizawa, Atsushi Ohshima, Alfred Scheidegger, Kenji Inagaki, Hidehiko Tanaka, Kenji Soda

Research output: Contribution to journalArticle

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Abstract

The nucleotide sequence of the alanine racemase (EC 5.1.1.1) gene from a thermophile, Bacillus stearothermophilus, was determined by the dideoxy chain termination method with universal and synthetic site-specific primers. The amino acid sequence of the enzyme predicted from the nucleotide sequence was confirmed by peptide sequence information derived from the N-terminal amino acid residues and several tryptic fragments. The alanine racemase gene consists of 1158 base pairs encoding a protein of 386 amino acid residues; the molecular weight of the apoenzyme is estimated as 43341. The racemase gene of B. stearothermophilus has a closely similar size (1158 vs 1167 base pairs) to that of the gene of a mesophile, B. subtilis, but shows a higher preference for codons ending in G or C. A comparison of the amino acid sequence with those of Bacillus subtilis and Salmonella typhimurium dadB and alr enzymes revealed overall sequence homologies of 31-54%, including an identical octapeptide bearing the pyridoxal 5′-phosphate binding site. Although the residues common in the four racemases are not continuously arrayed, these constitute distinct domains and their hydropathy profiles are very similar. The secondary structure of B. stearothermophilus alanine racemase was predicted from the results obtained by theoretical analysis and circular dichroism measurement.

Original languageEnglish
Pages (from-to)1311-1316
Number of pages6
JournalBiochemistry
Volume27
Issue number4
Publication statusPublished - 1988

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Alanine Racemase
Geobacillus stearothermophilus
Protein Sequence Analysis
Bacilli
DNA Sequence Analysis
Genes
Racemases and Epimerases
Amino Acids
DNA
Base Pairing
Amino Acid Sequence
Proteins
Bearings (structural)
Nucleotides
Apoenzymes
Salmonella
Pyridoxal Phosphate
Enzymes
Salmonella typhimurium
Sequence Homology

ASJC Scopus subject areas

  • Biochemistry

Cite this

Thermostable alanine racemase from Bacillus stearothermophilus : DNA and protein sequence determination and secondary structure prediction. / Tanizawa, Katsuyuki; Ohshima, Atsushi; Scheidegger, Alfred; Inagaki, Kenji; Tanaka, Hidehiko; Soda, Kenji.

In: Biochemistry, Vol. 27, No. 4, 1988, p. 1311-1316.

Research output: Contribution to journalArticle

Tanizawa, Katsuyuki ; Ohshima, Atsushi ; Scheidegger, Alfred ; Inagaki, Kenji ; Tanaka, Hidehiko ; Soda, Kenji. / Thermostable alanine racemase from Bacillus stearothermophilus : DNA and protein sequence determination and secondary structure prediction. In: Biochemistry. 1988 ; Vol. 27, No. 4. pp. 1311-1316.
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