8I8I

Crystal structure of Phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 A resolution

Replaces:  7WGJ

Summary for 8I8I

• Entry DOI: 10.2210/pdb8i8i/pdb
• Descriptor: Phosphopantetheine adenylyltransferase, 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: coad, ppat, transferase, coenzyme a biosynthesis
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 3
• Total formula weight: 53115.70

Authors

Ahmad, N.,Singh, P.K.,Sharma, P.,Sharma, S.,Singh, T.P. (deposition date: 2023-02-04, release date: 2023-02-22, Last modification date: 2024-04-10)

Primary citation

Ahmad, N.,Sharma, P.,Sharma, S.,Singh, T.P.
Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59 angstrom resolution.
Eur.Biophys.J., 53:147-157, 2024

PubMed Abstract: Phosphopantetheine adenylyltransferase (EC. 2.7.7.3, PPAT) catalyzes the penultimate step of the multistep reaction in the coenzyme A (CoA) biosynthesis pathway. In this step, an adenylyl group from adenosine triphosphate (ATP) is transferred to 4'-phosphopantetheine (PNS) yielding 3'-dephospho-coenzyme A (dpCoA) and pyrophosphate (PP). PPAT from strain C3 of Klebsiella pneumoniae (KpPPAT) was cloned, expressed and purified. It was crystallized using 0.1 M HEPES buffer and PEG10000 at pH 7.5. The crystals belonged to tetragonal space group P422 with cell dimensions of a = b = 72.82 Å and c = 200.37 Å. The structure was determined using the molecular replacement method and refined to values of 0.208 and 0.255 for R and R factors, respectively. The structure determination showed the presence of three crystallographically independent molecules A, B and C in the asymmetric unit. The molecules A and B are observed in the form of a dimer in the asymmetric unit while molecule C belongs to the second dimer whose partner is related by crystallographic twofold symmetry. The polypeptide chain of KpPPAT folds into a β/α structure. The conformations of the side chains of several residues in the substrate binding site in KpPPAT are significantly different from those reported in other PPATs. As a result, the modes of binding of substrates, phosphopantetheine (PNS) and adenosine triphosphate (ATP) differ considerably. The binding studies using fluorescence spectroscopy indicated a K value of 3.45 × 10 M for ATP which is significantly lower than the corresponding values reported for PPAT from other species.

PubMed: 38456905
DOI: 10.1007/s00249-024-01703-1

Experimental method

X-RAY DIFFRACTION (2.59 Å)