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Structure paper

TitleFilamentation modulates allosteric regulation of PRPS.
Journal, issue, pagesElife, Vol. 11, Year 2022
Publish dateJun 23, 2022
AuthorsHuan-Huan Hu / Guang-Ming Lu / Chia-Chun Chang / Yilan Li / Jiale Zhong / Chen-Jun Guo / Xian Zhou / Boqi Yin / Tianyi Zhang / Ji-Long Liu /
PubMed AbstractPhosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP ...Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP synthase (PRPS) is associated with human disorders, including Arts syndrome, retinal dystrophy, and gouty arthritis. Recent studies have demonstrated that PRPS can form filamentous cytoophidia in eukaryotes. Here, we show that PRPS forms cytoophidia in prokaryotes both in vitro and in vivo. Moreover, we solve two distinct filament structures of PRPS at near-atomic resolution using Cryo-EM. The formation of the two types of filaments is controlled by the binding of different ligands. One filament type is resistant to allosteric inhibition. The structural comparison reveals conformational changes of a regulatory flexible loop, which may regulate the binding of the allosteric inhibitor and the substrate ATP. A noncanonical allosteric AMP/ADP binding site is identified to stabilize the conformation of the regulatory flexible loop. Our findings not only explore a new mechanism of PRPS regulation with structural basis, but also propose an additional layer of cell metabolism through PRPS filamentation.
External linksElife / PubMed:35736577 / PubMed Central
MethodsEM (single particle)
Resolution2.3 - 2.9 Å
Structure data

33305

7xmu

EMDB-33305, PDB-7xmu:
E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A filament bound with ADP, Pi and R5P
Method: EM (single particle) / Resolution: 2.3 Å

33306

7xmv

EMDB-33306, PDB-7xmv:
E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A(AMP/ADP) filament bound with ADP, AMP and R5P
Method: EM (single particle) / Resolution: 2.6 Å

33309

7xn3

EMDB-33309, PDB-7xn3:
E.coli phosphoribosylpyrophosphate (PRPP) synthetase type B filament bound with Pi
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-HSX:
5-O-phosphono-alpha-D-ribofuranose

ChemComp-MG:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-HOH:
WATER / Water

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

Source
  • escherichia coli str. k-12 substr. mg1655 (bacteria)
KeywordsBIOSYNTHETIC PROTEIN / Allosteric enzyme / Kinase / Transferase / Nucleotide biosynthesis / ATP-binding / Magnesium / Manganese / Metal-binding / Nucleotide-binding

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