3r0x | pdb_00003r0x

Crystal structure of Selenomethionine incorporated apo D-serine deaminase from Salmonella tyhimurium

spinqualitylabelsall models 3r0x, resolution 1.93Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3r0x is a 1 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.93Å Ligands: EDO, MSE, NA, SO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function SDHD_SALTY Publication Abstract from PubMed 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 catalyzes 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 beta 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 co-factor, 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 found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modeling suggests that Thr 166 may be involved in abstraction of proton from the Calpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses alpha, beta elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates. Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis.,Bharath SR, Bisht S, Savithri HS, Murthy MR FEBS J. 2011 Jun 10. doi: 10.1111/j.1742-4658.2011.08210.x. PMID:21668644 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Deaminase 3D structures

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