3G6W

Asymetric GTP bound structure of UPRTase from Sulfolobus solfataricus containing PRPP-mg2+ in half of the active sites and R5P and PPi in the other half


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and kinetic studies of the allosteric transition in Sulfolobus solfataricus uracil phosphoribosyltransferase: Permanent activation by engineering of the C-terminus

Christoffersen, S.Kadziola, A.Johansson, E.Rasmussen, M.Willemoes, M.Jensen, K.F.

(2009) J.Mol.Biol. 393: 464-477

  • DOI: 10.1016/j.jmb.2009.08.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uracil phosphoribosyltransferase catalyzes the conversion of 5-phosphoribosyl-alpha-1-diphosphate (PRPP) and uracil to uridine monophosphate (UMP) and diphosphate (PP(i)). The tetrameric enzyme from Sulfolobus solfataricus has a unique type of allost ...

    Uracil phosphoribosyltransferase catalyzes the conversion of 5-phosphoribosyl-alpha-1-diphosphate (PRPP) and uracil to uridine monophosphate (UMP) and diphosphate (PP(i)). The tetrameric enzyme from Sulfolobus solfataricus has a unique type of allosteric regulation by cytidine triphosphate (CTP) and guanosine triphosphate (GTP). Here we report two structures of the activated state in complex with GTP. One structure (refined at 2.8-A resolution) contains PRPP in all active sites, while the other structure (refined at 2.9-A resolution) has PRPP in two sites and the hydrolysis products, ribose-5-phosphate and PP(i), in the other sites. Combined with three existing structures of uracil phosphoribosyltransferase in complex with UMP and the allosteric inhibitor cytidine triphosphate (CTP), these structures provide valuable insight into the mechanism of allosteric transition from inhibited to active enzyme. The regulatory triphosphates bind at a site in the center of the tetramer in a different manner and change the quaternary arrangement. Both effectors contact Pro94 at the beginning of a long beta-strand in the dimer interface, which extends into a flexible loop over the active site. In the GTP-bound state, two flexible loop residues, Tyr123 and Lys125, bind the PP(i) moiety of PRPP in the neighboring subunit and contribute to catalysis, while in the inhibited state, they contribute to the configuration of the active site for UMP rather than PRPP binding. The C-terminal Gly216 participates in a hydrogen-bond network in the dimer interface that stabilizes the inhibited, but not the activated, state. Tagging the C-terminus with additional amino acids generates an endogenously activated enzyme that binds GTP without effects on activity.


    Related Citations: 
    • Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus.
      Arent, S.,Harris, P.,Jensen, K.F.,Larsen, S.
      (2005) Biochemistry 44: 883


    Organizational Affiliation

    Department of Biology, University of Copenhagen, Biocenter, Copenhagen N, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil phosphoribosyltransferase
A, B, C, D
216Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: upp
EC: 2.4.2.9
Find proteins for Q980Q4 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q980Q4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
B, C
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
HSX
Query on HSX

Download SDF File 
Download CCD File 
B, C, D
5-O-phosphono-alpha-D-ribofuranose
C5 H11 O8 P
KTVPXOYAKDPRHY-AIHAYLRMSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, B, D
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
PRP
Query on PRP

Download SDF File 
Download CCD File 
A, D
ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.038α = 90.00
b = 98.758β = 92.80
c = 73.528γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Data collection, Refinement description