6CZF

The structure of E. coli PurF in complex with ppGpp-Mg

Summary for 6CZF

• Entry DOI: 10.2210/pdb6czf/pdb
• Descriptor: Amidophosphoribosyltransferase, MAGNESIUM ION, GUANOSINE-5',3'-TETRAPHOSPHATE, ... (4 entities in total)
• Functional Keywords: purf, ppgpp, transferase
• Biological source: Escherichia coli (strain K12)
• Total number of polymer chains: 4
• Total formula weight: 224150.77

Authors

Wang, B.,Grant, R.A.,Laub, M.T. (deposition date: 2018-04-09, release date: 2018-10-10, Last modification date: 2023-10-04)

Primary citation

Wang, B.,Dai, P.,Ding, D.,Del Rosario, A.,Grant, R.A.,Pentelute, B.L.,Laub, M.T.
Affinity-based capture and identification of protein effectors of the growth regulator ppGpp.
Nat. Chem. Biol., 15:141-150, 2019

PubMed Abstract: The nucleotide ppGpp is a highly conserved regulatory molecule in bacteria that helps tune growth rate to nutrient availability. Despite decades of study, how ppGpp regulates growth remains poorly understood. Here, we developed and validated a capture-compound mass spectrometry approach that identified >50 putative ppGpp targets in Escherichia coli. These targets control many key cellular processes and include 13 enzymes required for nucleotide synthesis. We demonstrated that ppGpp inhibits the de novo synthesis of all purine nucleotides by directly targeting the enzyme PurF. By solving a structure of PurF bound to ppGpp, we designed a mutation that ablates ppGpp-based regulation, leading to dysregulation of purine-nucleotide synthesis following ppGpp accumulation. Collectively, our results provide new insights into ppGpp-based growth control and a nearly comprehensive set of targets for future exploration. The capture compounds developed should also enable the rapid identification of ppGpp targets in any species, including pathogens.

PubMed: 30559427
DOI: 10.1038/s41589-018-0183-4

Experimental method

X-RAY DIFFRACTION (1.949 Å)