5XX1

Crystal structure of Arginine decarboxylase (AdiA) from Salmonella typhimurium

Summary for 5XX1

• Entry DOI: 10.2210/pdb5xx1/pdb
• Descriptor: Arginine decarboxylase, PHOSPHATE ION (3 entities in total)
• Functional Keywords: decamer, phosphate bound, salmonella typhimurium, loop movement, acid stress, lyase
• Biological source: Salmonella typhi
• Total number of polymer chains: 10
• Total formula weight: 845780.18

Authors

Deka, G.,Bharath, S.R.,Shavithri, H.S.,Murthy, M.R.N. (deposition date: 2017-06-30, release date: 2018-05-16, Last modification date: 2024-10-09)

Primary citation

Deka, G.,Bharath, S.R.,Savithri, 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

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: 28694189
DOI: 10.1016/j.bbrc.2017.07.032

Experimental method

X-RAY DIFFRACTION (3.1 Å)