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Conserved supersecondary structural motif in NAD-dependent dehydrogenases
A S Kutzenko1, V S Lamzin, V O Popov
1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow.
FEBS Letters
|March 20, 1998
Summary
Nicotinamide adenine dinucleotide (NAD)-dependent dehydrogenases, both L- and D-specific, share structural similarities within the Rossmann fold superfamily. A new classification parameter reveals conserved supersecondary structural motifs in these enzymes.
Area of Science:
- Biochemistry
- Structural Biology
- Enzymology
Background:
- L- and D-specific nicotinamide adenine dinucleotide (NAD)-dependent dehydrogenases are crucial enzymes.
- These enzymes are known to belong to the same structural protein superfamily, characterized by Rossmann fold domains.
- Understanding their structural relationships is key to enzyme classification and function.
Purpose of the Study:
- To propose a detailed classification of NAD-dependent dehydrogenase domains.
- To investigate the structural homology between catalytic and coenzyme binding domains in D-specific dehydrogenases.
- To identify and characterize conserved supersecondary structural motifs within the dehydrogenase superfamily.
Main Methods:
- Utilized the Structural Classification of Proteins (SCOP) database for protein structural analysis.
- Developed and applied a novel diagnostic parameter based on root-mean-square deviation (rms) per aligned pair for domain classification.
- Performed comparative structural analysis to identify conserved motifs and homologies.
Main Results:
- L- and D-specific NAD-dependent dehydrogenases were confirmed to map to the same structural protein superfamily based on Rossmann fold domains.
- A detailed classification scheme for these domains was proposed using the novel rms-based parameter.
- Strong structural homology was observed between the catalytic domain and the coenzyme binding domain in D-specific dehydrogenases.
- A conserved supersecondary structural motif, including a 5-stranded beta-sheet and alpha-helices, was identified within the superfamily.
Conclusions:
- The study provides a refined classification of NAD-dependent dehydrogenase domains.
- Structural homology between catalytic and coenzyme binding domains highlights evolutionary or functional relationships.
- The identified conserved supersecondary structure represents a fundamental architectural feature of the dehydrogenase superfamily.