Sequence and homology model of 3-isopropylmalate dehydrogenase from the psychrotrophic bacterium Vibrio sp. I5 suggest reasons for thermal instability

• Published in: Protein engineering 1997-06, Vol.10 (6), p.665-672
• Main Authors: Wallon, G, Lovett, S T, Magyar, C, Svingor, A, Szilagyi, A, Zàvodszky, P, Ringe, D, Petsko, G A
• Format: Article
• Language: English
• Subjects: 3-Isopropylmalate Dehydrogenase; Alcohol Oxidoreductases - chemistry; Alcohol Oxidoreductases - genetics; Alcohol Oxidoreductases - isolation & purification; Amino Acid Sequence; Arctic Regions; Cloning, Molecular; Hot Temperature; Leucine - genetics; Models, Molecular; Molecular Sequence Data; Protein Structure, Tertiary; Seawater; Sequence Alignment; Sequence Analysis; Sequence Homology, Amino Acid; Structure-Activity Relationship; Vibrio - enzymology; Vibrio - physiology
• ISSN: 0269-2139; 1741-0126; 1741-0134
• DOI: 10.1093/protein/10.6.665

The leuB gene from the psychrotrophic strain Vibrio sp. I5 has been cloned and sequenced. The gene codes for 3-isopropylmalate dehydrogenase, a 360-residue, dimeric enzyme involved in the biosynthesis of leucine. Three recently solved homologous isopropylmalate dehydrogenase (IPMDH) crystal structures from thermophilic and mesophilic organisms have been used to build a homology model for the psychrotrophic IPMDH and to deduce the possible structural reasons for its decreased thermostability. According to our model the psychrotrophic IPMDH contains fewer stabilizing interactions than its mesophilic and thermophilic counterparts. Elements that have been identified as destabilizing in the comparison of the psychrotrophic, mesophilic and thermophilic IPMDHs are a smaller number of salt-bridges, a reduction in aromatic-aromatic interactions, fewer proline residues and longer surface loops. In addition, there are a number of substitutions of otherwise strictly conserved residues that can be linked to thermostability.