5YH7

Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2.0 A resolution

Summary for 5YH7

• Entry DOI: 10.2210/pdb5yh7/pdb
• Descriptor: Phosphopantetheine adenylyltransferase, COENZYME A, SULFATE ION, ... (4 entities in total)
• Functional Keywords: transferase
• Biological source: Acinetobacter baumannii (strain ACICU)
• Total number of polymer chains: 1
• Total formula weight: 19534.76

Authors

Singh, P.K.,Gupta, A.,Kaur, P.,Sharma, S.,Singh, T.P. (deposition date: 2017-09-27, release date: 2017-10-11, Last modification date: 2023-11-22)

Primary citation

Gupta, A.,Singh, P.K.,Iqbal, N.,Sharma, P.,Baraigya, H.R.,Kaur, P.,Umar, M.S.,Ahmad, F.,Sharma, A.,Owais, M.,Sharma, S.,Singh, T.P.
Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii.
Biochim Biophys Acta Proteins Proteom, 1867:537-547, 2019

PubMed Abstract: Phosphopantetheine adenylyltransferase (PPAT, EC. 2.7.7.3) catalyzes an essential step in the reaction that transfers an adenylyl group from adenosine tri phosphate (ATP) to 4'-phosphopantetheine (pPant) yielding 3'- dephospho-coenzyme A (dPCoA) and pyrophosphate (PP) in the coenzyme A (CoA) biosynthesis pathway The enzyme PPAT from Acinetobacter baumannii (AbPPAT) was cloned, expressed and purified. The binding studies of AbPPAT were carried out with two compounds, tri‑sodium citrate (TSC) and l-ascorbic acid (LAA, vitamin-C) using fluorescence spectroscopic (FS) and surface Plasmon resonance (SPR) methods. Both methods provided similar values of dissociation constants for TSC and LAA which were of the order of 10 M and 10 M respectively. The computer aided docking studies indicated fewer interactions of LAA with AbPPAT as compared to those of TSC. The freshly purified samples of AbPPAT were crystallized. The crystals of AbPPAT were soaked in the solutions containing TSC and LAA. However, the crystals of the complex of AbPPAT with LAA did not diffract well and hence the structure of the complex of AbPPAT with LAA could not be determined. On the other hand, the crystals of the complex of AbPPAT with TSC diffracted well and the structure was determined at 1.76 Å resolution. It showed that TSC bound to AbPPAT at the ATP binding site and formed several intermolecular contacts including 12 hydrogen bonds. The results of binding studies for both TSC and LAA and the structure of the complex of AbPPAT with TSC clearly indicated a potential role of TSC and LAA as antibacterial agents.

PubMed: 30885618
DOI: 10.1016/j.bbapap.2019.03.002

Experimental method

X-RAY DIFFRACTION (2.03 Å)