4d9b | pdb_00004d9b

Pyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimurium D-Cysteine desulfhydrase obtained after co-crystallization with D-cycloserine

spinqualitylabelsall models 4d9b, resolution 1.67Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4d9b is a 4 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. Ligands: BEN, EDO, PMP Related: 4d8t, 4d8u, 4d8w, 4d92, 4d96, 4d97, 4d99, 4d9c, 4d9e, 4d9f Gene: dcyD, STM1953 (Salmonella enterica subsp. enterica serovar Typhimurium) Activity: D-cysteine desulfhydrase, with EC number 4.4.1.15 Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed Salmonella typhimurium DCyD (StDCyD) is a fold type II pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes the degradation of D-Cys to H(2)S and pyruvate. It also efficiently degrades beta-chloro-D-alanine (betaCDA). D-Ser is a poor substrate while the enzyme is inactive with respect to L-Ser and 1-amino-1-carboxy cyclopropane (ACC). Here, we report the X-ray crystal structures of StDCyD and of crystals obtained in the presence of D-Cys, betaCDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 A. The polypeptide fold of StDCyD consisting of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) resembles other fold type II PLP dependent enzymes. The structures obtained in the presence of D-Cys and betaCDA show the product, pyruvate, bound at a site 4.0-6.0 A away from the active site. ACC forms an external aldimine complex while D- and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at Calpha proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggest formation of PMP by the hydrolysis of cycloserines. Mutational studies suggest that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for Calpha proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed. Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase.,Bharath SR, Bisht S, Harijan RK, Savithri HS, Murthy MR PLoS One. 2012;7(5):e36267. Epub 2012 May 4. PMID:22574144 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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