3S5J

2.0A Crystal structure of human phosphoribosyl pyrophosphate synthetase 1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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Literature

Crystal and EM Structures of Human Phosphoribosyl Pyrophosphate Synthase I (PRS1) Provide Novel Insights into the Disease-Associated Mutations

Chen, P., Liu, Z., Wang, X., Peng, J., Sun, Q., Li, J., Wang, M., Niu, L., Zhang, Z., Cai, G., Teng, M., Li, X.

(2015) PLoS One 10: e0120304-e0120304

  • DOI: 10.1371/journal.pone.0120304
  • Primary Citation of Related Structures:  
    3S5J, 4LYG, 4LZN, 4LZO, 4M0P, 4M0U

  • PubMed Abstract: 

    • Human PRS1, which is indispensable for the biosynthesis of nucleotides, deoxynucleotides and their derivatives, is associated directly with multiple human diseases because of single base mutation. However, a molecular understanding of the effect of these mutations is hampered by the lack of understanding of its catalytic mechanism ...

    Human PRS1, which is indispensable for the biosynthesis of nucleotides, deoxynucleotides and their derivatives, is associated directly with multiple human diseases because of single base mutation. However, a molecular understanding of the effect of these mutations is hampered by the lack of understanding of its catalytic mechanism. Here, we reconstruct the 3D EM structure of the PRS1 apo state. Together with the native stain EM structures of AMPNPP, AMPNPP and R5P, ADP and the apo states with distinct conformations, we suggest the hexamer is the enzymatically active form. Based on crystal structures, sequence analysis, mutagenesis, enzyme kinetics assays, and MD simulations, we reveal the conserved substrates binding motifs and make further analysis of all pathogenic mutants.

    Organizational Affiliation: 

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China; Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People's Republic of China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribose-phosphate pyrophosphokinase 1B [auth A],
A [auth B]		326Homo sapiensMutation(s): 0 
Gene Names: PRPS1
EC: 2.7.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P60891 (Homo sapiens)
Explore P60891 
Go to UniProtKB:  P60891
PHAROS:  P60891
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60891
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.536α = 90
b = 170.536β = 90
c = 61.778γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references