7xmu

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E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A filament bound with ADP, Pi and R5P

Structural highlights

7xmu is a 6 chain structure with sequence from Escherichia coli str. K-12 substr. MG1655. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 2.3Å
Ligands:ADP, HSX, MG, PO4
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KPRS_ECOLI Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P).[HAMAP-Rule:MF_00583][1] [2] [3] [4] [5] [6] [7]

Publication Abstract from PubMed

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 E. coli 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.

Filamentation modulates allosteric regulation of PRPS.,Hu HH, Lu GM, Chang CC, Li Y, Zhong J, Guo CJ, Zhou X, Yin B, Zhang T, Liu JL Elife. 2022 Jun 23;11:e79552. doi: 10.7554/eLife.79552. PMID:35736577[8]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
1 reviews cite this structure
Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments.
Hvorecny et al. (2023)
0 more
2 other articles
No citations found

References

  1. ↑ Willemoes M, Hove-Jensen B, Larsen S. Steady state kinetic model for the binding of substrates and allosteric effectors to Escherichia coli phosphoribosyl-diphosphate synthase. J Biol Chem. 2000 Nov 10;275(45):35408-12. doi: 10.1074/jbc.M006346200. PMID:10954724 doi:http://dx.doi.org/10.1074/jbc.M006346200
  2. ↑ Bower SG, Harlow KW, Switzer RL, Hove-Jensen B. Characterization of the Escherichia coli prsA1-encoded mutant phosphoribosylpyrophosphate synthetase identifies a divalent cation-nucleotide binding site. J Biol Chem. 1989 Jun 15;264(17):10287-91. PMID:2542328
  3. ↑ Hove-Jensen B, Harlow KW, King CJ, Switzer RL. Phosphoribosylpyrophosphate synthetase of Escherichia coli. Properties of the purified enzyme and primary structure of the prs gene. J Biol Chem. 1986 May 25;261(15):6765-71. PMID:3009477
  4. ↑ Hove-Jensen B, Nygaard P. Phosphoribosylpyrophosphate synthetase of Escherichia coli, Identification of a mutant enzyme. Eur J Biochem. 1982 Aug;126(2):327-32. doi: 10.1111/j.1432-1033.1982.tb06782.x. PMID:6290219 doi:http://dx.doi.org/10.1111/j.1432-1033.1982.tb06782.x
  5. ↑ Hilden I, Hove-Jensen B, Harlow KW. Inactivation of Escherichia coli phosphoribosylpyrophosphate synthetase by the 2',3'-dialdehyde derivative of ATP. Identification of active site lysines. J Biol Chem. 1995 Sep 1;270(35):20730-6. doi: 10.1074/jbc.270.35.20730. PMID:7657655 doi:http://dx.doi.org/10.1074/jbc.270.35.20730
  6. ↑ Willemoes M, Nilsson D, Hove-Jensen B. Effects of mutagenesis of aspartic acid residues in the putative phosphoribosyl diphosphate binding site of Escherichia coli phosphoribosyl diphosphate synthetase on metal ion specificity and ribose 5-phosphate binding. Biochemistry. 1996 Jun 25;35(25):8181-6. doi: 10.1021/bi9528560. PMID:8679571 doi:http://dx.doi.org/10.1021/bi9528560
  7. ↑ Willemoes M, Hove-Jensen B. Binding of divalent magnesium by Escherichia coli phosphoribosyl diphosphate synthetase. Biochemistry. 1997 Apr 22;36(16):5078-83. doi: 10.1021/bi962610a. PMID:9125530 doi:http://dx.doi.org/10.1021/bi962610a
  8. ↑ Hu HH, Lu GM, Chang CC, Li Y, Zhong J, Guo CJ, Zhou X, Yin B, Zhang T, Liu JL. Filamentation modulates allosteric regulation of PRPS. Elife. 2022 Jun 23;11. pii: 79552. doi: 10.7554/eLife.79552. PMID:35736577 doi:http://dx.doi.org/10.7554/eLife.79552

Contents


PDB ID 7xmu

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