1HQO | pdb_00001hqo

CRYSTAL STRUCTURE OF THE NITROGEN REGULATION FRAGMENT OF THE YEAST PRION PROTEIN URE2P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.275 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.229 (DCC) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

The crystal structure of the nitrogen regulation fragment of the yeast prion protein Ure2p.

Umland, T.C.Taylor, K.L.Rhee, S.Wickner, R.B.Davies, D.R.

(2001) Proc Natl Acad Sci U S A 98: 1459-1464

  • DOI: https://doi.org/10.1073/pnas.98.4.1459
  • Primary Citation Related Structures: 
    1HQO

  • PubMed Abstract: 

    The yeast nonchromosomal gene [URE3] is due to a prion form of the nitrogen regulatory protein Ure2p. It is a negative regulator of nitrogen catabolism and acts by inhibiting the transcription factor Gln3p. Ure2p residues 1--80 are necessary for prion generation and propagation. The C-terminal fragment retains nitrogen regulatory activity, albeit somewhat less efficiently than the full-length protein, and it also lowers the frequency of prion generation. The crystal structure of this C-terminal fragment, Ure2p(97--354), at 2.3 A resolution is described here. It adopts the same fold as the glutathione S-transferase superfamily, consistent with their sequence similarity. However, Ure2p(97--354) lacks a properly positioned catalytic residue that is required for S-transferase activity. Residues within this regulatory fragment that have been indicated by mutational studies to influence prion generation have been mapped onto the three-dimensional structure, and possible implications for prion activity are discussed.


  • Organizational Affiliation
    • Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0560, USA.

Macromolecule Content 

  • Total Structure Weight: 59.88 kDa 
  • Atom Count: 3,868 
  • Modeled Residue Count: 450 
  • Deposited Residue Count: 516 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
URE2 PROTEIN
A, B
258Saccharomyces cerevisiaeMutation(s): 7 
Gene Names: URE2
EC: 1.8.4 (UniProt), 1.11.1.9 (UniProt)
UniProt
Find proteins for P23202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23202 
Go to UniProtKB:  P23202
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23202
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.275 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.229 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.31α = 90
b = 69.19β = 90
c = 149.99γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
SnBphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary