8DBK

Human PRPS1 with Phosphate, ATP, and R5P; Hexamer with resolved catalytic loops

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-06-14 Released: 2023-02-15 
  • Deposition Author(s): Hvorecny, K.L., Kollman, J.M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Human PRPS1 filaments stabilize allosteric sites to regulate activity.

Hvorecny, K.L.Hargett, K.Quispe, J.D.Kollman, J.M.

(2023) Nat Struct Mol Biol 30: 391-402

  • DOI: https://doi.org/10.1038/s41594-023-00921-z
  • Primary Citation of Related Structures:  
    8DBC, 8DBD, 8DBE, 8DBF, 8DBG, 8DBH, 8DBI, 8DBJ, 8DBK, 8DBL, 8DBM, 8DBN, 8DBO

  • PubMed Abstract: 

    The universally conserved enzyme phosphoribosyl pyrophosphate synthetase (PRPS) assembles filaments in evolutionarily diverse organisms. PRPS is a key regulator of nucleotide metabolism, and mutations in the human enzyme PRPS1 lead to a spectrum of diseases. Here we determine structures of human PRPS1 filaments in active and inhibited states, with fixed assembly contacts accommodating both conformations. The conserved assembly interface stabilizes the binding site for the essential activator phosphate, increasing activity in the filament. Some disease mutations alter assembly, supporting the link between filament stability and activity. Structures of active PRPS1 filaments turning over substrate also reveal coupling of catalysis in one active site with product release in an adjacent site. PRPS1 filaments therefore provide an additional layer of allosteric control, conserved throughout evolution, with likely impact on metabolic homeostasis. Stabilization of allosteric binding sites by polymerization adds to the growing diversity of assembly-based enzyme regulatory mechanisms.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribose-phosphate pyrophosphokinase 1
A, B, C, D, E
A, B, C, D, E, F
318Homo 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
GTEx:  ENSG00000147224 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60891
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth E],
FA [auth F],
G [auth A],
Q [auth C],
V [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PRP (Subject of Investigation/LOI)
Query on PRP

Download Ideal Coordinates CCD File 
L [auth B]1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
M [auth B]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
HSX (Subject of Investigation/LOI)
Query on HSX

Download Ideal Coordinates CCD File 
BA [auth E],
GA [auth F],
H [auth A],
R [auth C],
W [auth D]
5-O-phosphono-alpha-D-ribofuranose
C5 H11 O8 P
KTVPXOYAKDPRHY-AIHAYLRMSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
CA [auth E]
HA [auth F]
I [auth A]
N [auth B]
S [auth C]
CA [auth E],
HA [auth F],
I [auth A],
N [auth B],
S [auth C],
X [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
DA [auth E]
EA [auth E]
IA [auth F]
J [auth A]
JA [auth F]
DA [auth E],
EA [auth E],
IA [auth F],
J [auth A],
JA [auth F],
K [auth A],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
Y [auth D],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONPHENIX1.18

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesF32AI145111
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM118396

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2023-03-29
    Changes: Database references
  • Version 1.3: 2024-06-12
    Changes: Data collection