PDBsum entry 1r5m

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Transcription PDB id
Protein chain
351 a.a. *
SO4 ×2
Waters ×305
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Crystal structure of thE C-terminal wd40 domain of sif2
Structure: Sir4-interacting protein sif2. Chain: a. Fragment: c-terminal wd40 domain (residues 113-535). Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: sif2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.55Å     R-factor:   0.190     R-free:   0.204
Authors: D.Cerna,D.K.Wilson
Key ref:
D.Cerna and D.K.Wilson (2005). The structure of Sif2p, a WD repeat protein functioning in the SET3 corepressor complex. J Mol Biol, 351, 923-935. PubMed id: 16051270 DOI: 10.1016/j.jmb.2005.06.025
10-Oct-03     Release date:   01-Mar-05    
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Protein chain
Pfam   ArchSchema ?
P38262  (SIF2_YEAST) -  SIR4-interacting protein SIF2
535 a.a.
351 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1016/j.jmb.2005.06.025 J Mol Biol 351:923-935 (2005)
PubMed id: 16051270  
The structure of Sif2p, a WD repeat protein functioning in the SET3 corepressor complex.
D.Cerna, D.K.Wilson.
In Saccharomyces cerevisiae, the SIF2 gene product is an integral component of the Set3 complex (SET3C), an assembly of proteins with some homology to the human SMRT and N-CoR corepressor complexes. SET3C has histone deacetylase activity that is responsible for repressing a set of meiotic genes. We have determined the X-ray crystal structure of a 46 kDa C-terminal domain of a SET3C core protein, Sif2p to 1.55 A resolution and a crystallographic R-factor of 19.0%. This domain contains an unusual eight-bladed beta-propeller structure, which differs from other transcriptional corepressor structures such as yeast Tup1p and human groucho (Gro)/TLE1, which have only seven. We have demonstrated intact Sif2p is a tetramer and the N-terminal LisH (Lis-homology)-containing domain mediates tetramerization and interaction with another component of SET3C, Snt1p. Multiple sequence alignments indicate that a surface on the "top" of the protein is conserved among species, suggesting that it may play a common role in binding partner proteins. Since Sif2p appears to be the yeast homolog of human TBL1 and TBLR1, which function in the N-CoR/SMRT complexes, its structural and oligomeric properties are likely to be very similar.
  Selected figure(s)  
Figure 1.
Figure 1. Stereo view of the C-terminal domain of S. cerevisiae Sif2p (a) looking down the central axis of the eight WD blades at the "top" surface. The N and C termini are labeled. Main-chain disordered regions are marked by the last traceable residue number with black spheres. (b) Rotated 90° on the x-axis relative to the previous orientation. These are colored progressing from blue at the N terminus to red at the C terminus. This Figure was generated with MOLSCRIPT47 and Raster3D.48
Figure 2.
Figure 2. Structural and sequence conservation in Sif2p WD repeats. (a) Stereo view of all eight main-chain residues aligned with blade 5. Repeats are colored ranging from purple for repeat 1 to red for repeat 8. The WD repeat colored in black is blade 5 from the structure of Gb.49 This Figure was generated with MOLSCRIPT47 and Raster3D.48 (b) WD repeat consensus amino acid sequence (adapted from Smith et al.20) aligned to the Sif2p WD repeats.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 351, 923-935) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21240272 J.Oberoi, L.Fairall, P.J.Watson, J.C.Yang, Z.Czimmerer, T.Kampmann, B.T.Goult, J.A.Greenwood, J.T.Gooch, B.C.Kallenberger, L.Nagy, D.Neuhaus, and J.W.Schwabe (2011).
Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery.
  Nat Struct Mol Biol, 18, 177-184.
PDB codes: 2l5g 2xtc 2xtd 2xte
19734367 C.Su, Y.Li, Y.Lu, and J.Chen (2009).
Mss11, a transcriptional activator, is required for hyphal development in Candida albicans.
  Eukaryot Cell, 8, 1780-1791.  
19377037 S.Ding, R.Mehrabi, C.Koten, Z.Kang, Y.Wei, K.Seong, H.C.Kistler, and J.R.Xu (2009).
Transducin beta-like gene FTL1 is essential for pathogenesis in Fusarium graminearum.
  Eukaryot Cell, 8, 867-876.  
18314376 Z.Liu, and V.Karmarkar (2008).
Groucho/Tup1 family co-repressors in plant development.
  Trends Plant Sci, 13, 137-144.  
17767906 J.M.Suh, D.Zeve, R.McKay, J.Seo, Z.Salo, R.Li, M.Wang, and J.M.Graff (2007).
Adipose is a conserved dosage-sensitive antiobesity gene.
  Cell Metab, 6, 195-207.  
17264208 J.Napetschnig, G.Blobel, and A.Hoelz (2007).
Crystal structure of the N-terminal domain of the human protooncogene Nup214/CAN.
  Proc Natl Acad Sci U S A, 104, 1783-1788.
PDB code: 2oit
16407068 B.A.Appleton, P.Wu, and C.Wiesmann (2006).
The crystal structure of murine coronin-1: a regulator of actin cytoskeletal dynamics in lymphocytes.
  Structure, 14, 87-96.
PDB codes: 2aq5 2b4e
16893456 X.M.Zhang, Q.Chang, L.Zeng, J.Gu, S.Brown, and R.S.Basch (2006).
TBLR1 regulates the expression of nuclear hormone receptor co-repressors.
  BMC Cell Biol, 7, 31.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.