4D9F

D-Cysteine desulfhydrase from Salmonella typhimurium complexed with D-cycloserine (DCS)

Summary for 4D9F

• Entry DOI: 10.2210/pdb4d9f/pdb
• Related: 4D8T 4D8U 4D8W 4D92 4D96 4D97 4D99 4D9B 4D9C 4D9E
• Descriptor: D-Cysteine desulfhydrase, BENZAMIDINE, D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE, ... (4 entities in total)
• Functional Keywords: fold type ii plp-dependent enzyme, tryptophan synthase beta subunit like family, lyase
• Biological source: Salmonella typhimurium
• Total number of polymer chains: 4
• Total formula weight: 147896.30

Authors

Bharath, S.R.,Shveta, B.,Rajesh, K.H.,Savithri, H.S.,Murthy, M.R.N. (deposition date: 2012-01-11, release date: 2012-05-30, Last modification date: 2023-11-08)

Primary citation

Bharath, S.R.,Bisht, S.,Harijan, R.K.,Savithri, H.S.,Murthy, M.R.N.
Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase.
Plos One, 7:e36267-e36267, 2012

PubMed Abstract: 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 β-chloro-D-alanine (βCDA). 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, βCDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 Å. 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 βCDA show the product, pyruvate, bound at a site 4.0-6.0 Å 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 Cα 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 Cα proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed.

PubMed: 22574144
DOI: 10.1371/journal.pone.0036267

Experimental method

X-RAY DIFFRACTION (2.61 Å)