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PDBsum entry 1hqo

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protein Protein-protein interface(s) links
Signaling protein PDB id
1hqo
Jmol
Contents
Protein chains
227 a.a. *
Waters ×204
* Residue conservation analysis
PDB id:
1hqo
Name: Signaling protein
Title: Crystal structure of the nitrogen regulation fragment of the yeast prion protein ure2p
Structure: Ure2 protein. Chain: a, b. Fragment: nitrogen regulation fragment. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ure2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.221     R-free:   0.275
Authors: T.C.Umland,K.L.Taylor,S.Rhee,R.B.Wickner,D.R.Davies
Key ref:
T.C.Umland et al. (2001). The crystal structure of the nitrogen regulation fragment of the yeast prion protein Ure2p. Proc Natl Acad Sci U S A, 98, 1459-1464. PubMed id: 11171973 DOI: 10.1073/pnas.041607898
Date:
18-Dec-00     Release date:   14-Feb-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23202  (URE2_YEAST) -  Transcriptional regulator URE2
Seq:
Struc:
354 a.a.
227 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.9  - Glutathione peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 glutathione + H2O2 = glutathione disulfide + 2 H2O
2 × glutathione
+ H(2)O(2)
= glutathione disulfide
+ 2 × H(2)O
      Cofactor: Se(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of nitrogen utilization   1 term 
  Biochemical function     transcription corepressor activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.041607898 Proc Natl Acad Sci U S A 98:1459-1464 (2001)
PubMed id: 11171973  
 
 
The crystal structure of the nitrogen regulation fragment of the yeast prion protein Ure2p.
T.C.Umland, K.L.Taylor, S.Rhee, R.B.Wickner, D.R.Davies.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Stereoview of the Ure2p(97-354). Monomer A is green and Monomer B is cyan. Prion-inhibiting regions (His-151 to Ser-158 and Val-347 to Glu-354) are indicated in blue, and the prion-promoting region (Ser-221 to Ile-227) is indicated in red. Gold labels the position of two additional residues implicated in affecting prion-induction, K127 and V271.
Figure 4.
Fig. 4. The superposition of Monomer A of Ure2p(97-354) (red) and a monomer of A. thaliana GST (38) (blue). This representation is viewed into the cleft between the two domains, which in GST contains the G- and H-sites.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21076138 L.Chen, L.J.Chen, H.Y.Wang, Y.Q.Wang, and S.Perrett (2011).
Deletion of a Ure2 C-terminal prion-inhibiting region promotes the rate of fibril seed formation and alters interaction with Hsp40.
  Protein Eng Des Sel, 24, 69-78.  
21219467 U.Baxa, P.W.Keller, N.Cheng, J.S.Wall, and A.C.Steven (2011).
In Sup35p filaments (the [PSI+] prion), the globular C-terminal domains are widely offset from the amyloid fibril backbone.
  Mol Microbiol, 79, 523-532.  
21419850 Y.Q.Wang, M.Bongiovanni, S.L.Gras, and S.Perrett (2011).
The fibrils of Ure2p homologs from Saccharomyces cerevisiae and Saccharoymyces paradoxus have similar cross-β structure in both dried and hydrated forms.
  J Struct Biol, 174, 505-511.  
21091436 Y.Yu, H.Y.Wang, M.Bai, and S.Perrett (2011).
Flexibility of the Ure2 prion domain is important for amyloid fibril formation.
  Biochem J, 434, 143-151.  
  20424506 A.Böckmann, and B.H.Meier (2010).
Prions: En route from structural models to structures.
  Prion, 4, 72-79.  
  20824085 C.Zhang, A.P.Jackson, Z.R.Zhang, Y.Han, S.Yu, R.Q.He, and S.Perrett (2010).
Amyloid-like aggregates of the yeast prion protein ure2 enter vertebrate cells by specific endocytotic pathways and induce apoptosis.
  PLoS One, 5, 0.  
19258323 L.Fei, and S.Perrett (2009).
Disulfide bond formation significantly accelerates the assembly of Ure2p fibrils because of the proximity of a potential amyloid stretch.
  J Biol Chem, 284, 11134-11141.  
19383475 L.Pieri, M.Bucciantini, P.Guasti, J.Savistchenko, R.Melki, and M.Stefani (2009).
Synthetic lipid vesicles recruit native-like aggregates and affect the aggregation process of the prion Ure2p: insights on vesicle permeabilization and charge selectivity.
  Biophys J, 96, 3319-3330.  
18322039 C.Gancedo, and C.L.Flores (2008).
Moonlighting proteins in yeasts.
  Microbiol Mol Biol Rev, 72, 197.  
18441120 K.H.Wong, M.J.Hynes, and M.A.Davis (2008).
Recent advances in nitrogen regulation: a comparison between Saccharomyces cerevisiae and filamentous fungi.
  Eukaryot Cell, 7, 917-925.  
17507672 F.Shewmaker, L.Mull, T.Nakayashiki, D.C.Masison, and R.B.Wickner (2007).
Ure2p function is enhanced by its prion domain in Saccharomyces cerevisiae.
  Genetics, 176, 1557-1565.  
17151465 B.Ono, M.Kubota, H.Kimiduka, H.Kawaminami, T.Ueto, S.Yokosawa, M.Iseda, Y.Yamamoto, Y.Murakami, and S.Yokota (2006).
Production of a polymer-forming fusion protein in Escerichia coli strain BL21.
  Biosci Biotechnol Biochem, 70, 2813-2823.  
17001037 N.Ranson, T.Stromer, L.Bousset, R.Melki, and L.C.Serpell (2006).
Insights into the architecture of the Ure2p yeast protein assemblies from helical twisted fibrils.
  Protein Sci, 15, 2481-2487.  
15869381 D.Davies, and D.Davies (2005).
A quiet life with proteins.
  Annu Rev Biophys Biomol Struct, 34, 1.  
16060675 J.C.Chan, N.A.Oyler, W.M.Yau, and R.Tycko (2005).
Parallel beta-sheets and polar zippers in amyloid fibrils formed by residues 10-39 of the yeast prion protein Ure2p.
  Biochemistry, 44, 10669-10680.  
15956663 N.Talarek, L.Maillet, C.Cullin, and M.Aigle (2005).
The [URE3] prion is not conserved among Saccharomyces species.
  Genetics, 171, 23-34.  
15806612 R.Rai, and T.G.Cooper (2005).
In vivo specificity of Ure2 protection from heavy metal ion and oxidative cellular damage in Saccharomyces cerevisiae.
  Yeast, 22, 343-358.  
16207084 S.Catharino, J.Buchner, and S.Walter (2005).
Characterization of oligomeric species in the fibrillization pathway of the yeast prion Ure2p.
  Biol Chem, 386, 633-641.  
15143215 A.V.Kajava, U.Baxa, R.B.Wickner, and A.C.Steven (2004).
A model for Ure2p prion filaments and other amyloids: the parallel superpleated beta-structure.
  Proc Natl Acad Sci U S A, 101, 7885-7890.  
15282319 E.D.Ross, U.Baxa, and R.B.Wickner (2004).
Scrambled prion domains form prions and amyloid.
  Mol Cell Biol, 24, 7206-7213.  
16117685 R.B.Wickner, H.K.Edskes, E.D.Ross, M.M.Pierce, F.Shewmaker, U.Baxa, and A.Brachmann (2004).
Prions of yeast are genes made of protein: amyloids and enzymes.
  Cold Spring Harb Symp Quant Biol, 69, 489-496.  
15355224 R.B.Wickner, H.K.Edskes, E.D.Ross, M.M.Pierce, U.Baxa, A.Brachmann, and F.Shewmaker (2004).
Prion genetics: new rules for a new kind of gene.
  Annu Rev Genet, 38, 681-707.  
12925776 A.Baudin-Baillieu, E.Fernandez-Bellot, F.Reine, E.Coissac, and C.Cullin (2003).
Conservation of the prion properties of Ure2p through evolution.
  Mol Biol Cell, 14, 3449-3458.  
12177423 H.K.Edskes, and R.B.Wickner (2002).
Conservation of a portion of the S. cerevisiae Ure2p prion domain that interacts with the full-length protein.
  Proc Natl Acad Sci U S A, 99, 16384-16391.  
12065404 L.Bousset, N.H.Thomson, S.E.Radford, and R.Melki (2002).
The yeast prion Ure2p retains its native alpha-helical conformation upon assembly into protein fibrils in vitro.
  EMBO J, 21, 2903-2911.  
12142498 S.M.Uptain, and S.Lindquist (2002).
Prions as protein-based genetic elements.
  Annu Rev Microbiol, 56, 703-741.  
11959975 U.Baxa, V.Speransky, A.C.Steven, and R.B.Wickner (2002).
Mechanism of inactivation on prion conversion of the Saccharomyces cerevisiae Ure2 protein.
  Proc Natl Acad Sci U S A, 99, 5253-5260.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.