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Protein Engineering, Vol. 15, No. 3, 215-223, March 2002
© 2002 Oxford University Press

A low-resolution 3D model of the tetrameric alcohol dehydrogenase from Sulfolobus solfataricus

Rita Casadio1, Pier Luigi Martelli1, Antonietta Giordano2, Mosè Rossi2,3 and Carlo A. Raia2,4

1 Laboratory of Biocomputing, Centro Interdipartimentale per le Ricerche Biotecnologiche (CIRB), Bologna and Laboratory of Biophysics, Department of Biology, University of Bologna, Via Irnerio 42, 40126 Bologna, 2 IBPE, Consiglio Nazionale delle Ricerche, Via G. Marconi 10, 80125 Naples and 3 Università di Napoli `Federico II', Via Mezzocannone 16, 80134 Naples, Italy

We describe the computation of a model of the thermophilic NAD-dependent homotetrameric alcohol dehydrogenase from the archaeon Sulfolobus solfataricus (SsADH). Modeling is based on the knowledge that each monomer contains two Zn ions with catalytic and structural function, respectively. In the database of known structures, proteins with similar functions are either dimers containing two zinc ions per monomer or tetramers with one zinc ion per monomer. In any case, the sequence identity of the target to the possible templates is low. A threading procedure is therefore developed which includes constraints taking into account residue conservation both at the zinc ion binding and at the monomer–monomer interaction sites in the tetrameric unit. The model is consistent with previously reported data. Furthermore, cross-linking experiments are described which support the computed tetrameric model.


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