6AA9
T166A mutant of D-Serine deaminase from Salmonella typhimurium
Summary for 6AA9
| Entry DOI | 10.2210/pdb6aa9/pdb |
| Descriptor | D-serine dehydratase, SODIUM ION, PHOSPHATE ION, ... (4 entities in total) |
| Functional Keywords | monomer, plp bound, salmonella typhimurium, deaminase, lyase |
| Biological source | Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) |
| Total number of polymer chains | 1 |
| Total formula weight | 48802.93 |
| Authors | Deka, G.,Bharath, S.R.,Shavithri, H.S.,Murthy, M.R.N. (deposition date: 2018-07-17, release date: 2019-07-17, Last modification date: 2023-11-22) |
| Primary citation | Deka, G.,Bharath, S.R.,Shavithri, H.S.,Murthy, M.R.N. Structural studies on the decameric S. typhimurium arginine decarboxylase (ADC): Pyridoxal 5'-phosphate binding induces conformational changes Biochem. Biophys. Res. Commun., 490:1362-1368, 2017 Cited by PubMed Abstract: Enteric pathogens such as Salmonella typhimurium colonize the human gut in spite of the lethal acidic pH environment (pH < 2.5) due to the activation of inducible acid tolerance response (ATR) systems. The pyridoxal 5'-phosphate (PLP)-dependent enzyme, biodegradative arginine decarboxylase (ADC, encoded by AdiA), is a component of an ATR system. The enzyme consumes a cytoplasmic proton in the process of arginine degradation to agmatine. Arginine-agmatine antiporter (AdiC) exchanges the product agmatine for arginine. In this manuscript, we describe the structure of Salmonella typhimurium ADC (StADC). The decameric structure assembled from five dimers related by a non crystallographic 5-fold symmetry represents the first apo-form of the enzyme. The structure suggests that PLP-binding is not a prerequisite for oligomerization. Comparison with E. coli ADC reveals that PLP-binding is accompanied by the movement and ordering of two loops (residues 150-159 and 191-197) and a few active site residues such as His256 and Lys257. A number of residues important for substrate binding are disordered in the apo-StADC structure indicating that PLP binding is important for substrate binding. Unlike the interactions between 5-fold related protomers, interactions that stabilize the dimeric structure are not pH dependent. PubMed: 28694189DOI: 10.1016/j.bbrc.2017.07.032 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.7 Å) |
Structure validation
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