tailieunhanh - Báo cáo khoa học: Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium – implications on substrate specificity and catalysis

Metabolism ofD-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimuriumD-serine deaminase (StDSD) is a pyridoxal 5¢ phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. | IFEBS Journal Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis Sakshibeedu Rajegowda Bharath1 Shveta Bisht1 Handanhal Subbarao Savithri2 and Mattur Ramabhadrashastry Narasimha Murthy1 1 Molecular Biophysics Unit Indian Institute of Science Bangalore India 2 Department of Biochemistry Indian Institute of Science Bangalore India Keywords D-serine deaminase open and closed conformations pyridoxal5 phosphate dependent Foldtype II enzyme X-ray diffraction a b elimination Correspondence M. R. N. Murthy Molecular Biophysics Unit Indian Institute of Science Bangalore 560 012 India Fax 91 80 2360 0535 Tel 91 80 2293 2458 E-mail mrn@ Received 12 March 2011 revised 29 May 2011 accepted 7 June 2011 doi Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-serine deaminase StDSD is a pyridoxal 5 phosphate PLP dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase b subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD WtDSD and selenomethionine labelled StDSD SeMetDSD significant electron density was not observed for the cofactor indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD crystallized in the presence of isoserine was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was .