PDBsum entry 2fq3

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protein links
Transcription PDB id
Protein chain
85 a.a. *
Waters ×123
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Structure and function of the swirm domain, a conserved protein module found in chromatin regulatory complexes
Structure: Transcription regulatory protein swi3. Chain: a. Fragment: swirm domain. Synonym: swi/snf complex component swi3, transcription factor tye2. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: swi3, tye2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.40Å     R-factor:   0.207     R-free:   0.213
Authors: G.Da,J.Lenkart,K.Zhao,R.Shiekhattar,B.R.Cairns,R.Marmorstein
Key ref:
G.Da et al. (2006). Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc Natl Acad Sci U S A, 103, 2057-2062. PubMed id: 16461455 DOI: 10.1073/pnas.0510949103
17-Jan-06     Release date:   07-Feb-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P32591  (SWI3_YEAST) -  SWI/SNF complex subunit SWI3
825 a.a.
85 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     DNA binding     1 term  


DOI no: 10.1073/pnas.0510949103 Proc Natl Acad Sci U S A 103:2057-2062 (2006)
PubMed id: 16461455  
Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes.
G.Da, J.Lenkart, K.Zhao, R.Shiekhattar, B.R.Cairns, R.Marmorstein.
The SWIRM domain is a module found in the Swi3 and Rsc8 subunits of SWI/SNF-family chromatin remodeling complexes, and the Ada2 and BHC110/LSD1 subunits of chromatin modification complexes. Here we report the high-resolution crystal structure of the SWIRM domain from Swi3 and characterize the in vitro and in vivo function of the SWIRM domains from Saccharomyces cerevisiae Swi3 and Rsc8. The Swi3 SWIRM forms a four-helix bundle containing a pseudo 2-fold axis and a helix-turn-helix motif commonly found in DNA-binding proteins. We show that the Swi3 SWIRM binds free DNA and mononucleosomes with high and comparable affinity and that a subset of Swi3 substitution mutants that display growth defects in vivo also show impaired DNA-binding activity in vitro, consistent with a nucleosome targeting function of this domain. Genetic and biochemical studies also reveal that the Rsc8 and Swi3 SWIRM domains are essential for the proper assembly and in vivo functions of their respective complexes. Together, these studies identify the SWIRM domain as an essential multifunctional module for the regulation of gene expression.
  Selected figure(s)  
Figure 3.
Fig. 3. Growth phenotypes and stability/assembly properties of swi3 SWIRM mutants. (A) Growth phenotypes of SWIRM domain mutants. A swi3 strain (YBC2051) was transformed with LEU2-bearing plasmids containing either SWI3 or swi3^S derivatives, and tested for growth ability on various media and conditions (as indicated). (B) Stability and assembly properties of SWIRM domain mutants. Swi3 derivative expression (Upper) and Swi3 derivative assembly into SWI/SNF (Lower) are shown.
Figure 4.
Fig. 4. In vitro and in vivo characterization of putative Swi3 SWIRM domain DNA-binding mutants. (A) Results of DNA-binding assays using recombinant GST-Swi3 SWIRM domain and substitution mutants. The assay was carried out as described in Fig. 2B, and the substitution mutants of the Swi3-SWIRM domain used in the assay are indicated. The dissociation constant calculated from the binding data for GST-Swi3 SWIRM: cruciform DNA is 105.36 ± 7.65 nM. CD spectra of native and GST-SWIRM domain mutants are essentially superimposable, suggesting that the SWIRM domain mutants are properly folded (data not shown). (B) The Swi3 SWIRM double mutation K383D K387D fails to grow on media lacking inositol at elevated temperatures. A swi3 strain (YBC2051) was transformed with LEU2-bearing plasmids containing the K derivatives, grown on synthetic medium lacking leucine, and then spotted in 10-fold serial dilutions on a medium lacking inositol, and grown at either 23°C or 35°C for 4 days. (C) Model for a Swi3 SWIRM domain/DNA complex. The model for the protein/DNA complex was created by superimposing the helix-turn-helix of the Swi3 SWIRM domain (green) with the c-Myb/DNA complex. The DNA from C-Myb is shown in red, and the c-Myb protein is removed for clarity. Residues of the Swi3 SWIRM implicated for DNA binding from the in vivo and in vitro studies (D374, K383, K387, and N392A) are highlighted as blue side chains.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20819789 N.Depège-Fargeix, M.Javelle, P.Chambrier, N.Frangne, D.Gerentes, P.Perez, P.M.Rogowsky, and V.Vernoud (2011).
Functional characterization of the HD-ZIP IV transcription factor OCL1 from maize.
  J Exp Bot, 62, 293-305.  
  20644220 D.Lang, B.Weiche, G.Timmerhaus, S.Richardt, D.M.Riaño-Pachón, L.G.Corrêa, R.Reski, B.Mueller-Roeber, and S.A.Rensing (2010).
Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.
  Genome Biol Evol, 2, 488-503.  
21124763 S.Pu, A.L.Turinsky, J.Vlasblom, T.On, X.Xiong, A.Emili, Z.Zhang, J.Greenblatt, J.Parkinson, and S.J.Wodak (2010).
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.
  PLoS One, 5, e14122.  
20101264 Z.Yang, J.Jiang, D.M.Stewart, S.Qi, K.Yamane, J.Li, Y.Zhang, and J.Wong (2010).
AOF1 is a histone H3K4 demethylase possessing demethylase activity-independent repression function.
  Cell Res, 20, 276-287.  
19407342 A.Karytinos, F.Forneris, A.Profumo, G.Ciossani, E.Battaglioli, C.Binda, and A.Mattevi (2009).
A novel mammalian flavin-dependent histone demethylase.
  J Biol Chem, 284, 17775-17782.  
18936164 A.M.Gamper, J.Kim, and R.G.Roeder (2009).
The STAGA subunit ADA2b is an important regulator of human GCN5 catalysis.
  Mol Cell Biol, 29, 266-280.  
19624733 F.Forneris, E.Battaglioli, A.Mattevi, and C.Binda (2009).
New roles of flavoproteins in molecular cell biology: histone demethylase LSD1 and chromatin.
  FEBS J, 276, 4304-4312.  
19223330 Y.He, R.Imhoff, A.Sahu, and I.Radhakrishnan (2009).
Solution structure of a novel zinc finger motif in the SAP30 polypeptide of the Sin3 corepressor complex and its potential role in nucleic acid recognition.
  Nucleic Acids Res, 37, 2142-2152.
PDB code: 2kdp
18343668 F.Forneris, C.Binda, E.Battaglioli, and A.Mattevi (2008).
LSD1: oxidative chemistry for multifaceted functions in chromatin regulation.
  Trends Biochem Sci, 33, 181-189.  
17851108 J.C.Culhane, and P.A.Cole (2007).
LSD1 and the chemistry of histone demethylation.
  Curr Opin Chem Biol, 11, 561-568.  
17462898 L.Di Stefano, J.Y.Ji, N.S.Moon, A.Herr, and N.Dyson (2007).
Mutation of Drosophila Lsd1 disrupts H3-K4 methylation, resulting in tissue-specific defects during development.
  Curr Biol, 17, 808-812.  
17707232 P.Zhu, W.Zhou, J.Wang, J.Puc, K.A.Ohgi, H.Erdjument-Bromage, P.Tempst, C.K.Glass, and M.G.Rosenfeld (2007).
A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation.
  Mol Cell, 27, 609-621.  
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
17306844 V.K.Gangaraju, and B.Bartholomew (2007).
Mechanisms of ATP dependent chromatin remodeling.
  Mutat Res, 618, 3.  
17567753 Z.Chen, J.Zang, J.Kappler, X.Hong, F.Crawford, Q.Wang, F.Lan, C.Jiang, J.Whetstine, S.Dai, K.Hansen, Y.Shi, and G.Zhang (2007).
Structural basis of the recognition of a methylated histone tail by JMJD2A.
  Proc Natl Acad Sci U S A, 104, 10818-10823.
PDB codes: 2p5b 2pxj
16885027 M.Yang, C.B.Gocke, X.Luo, D.Borek, D.R.Tomchick, M.Machius, Z.Otwinowski, and H.Yu (2006).
Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase.
  Mol Cell, 23, 377-387.
PDB code: 2iw5
16799558 P.Stavropoulos, G.Blobel, and A.Hoelz (2006).
Crystal structure and mechanism of human lysine-specific demethylase-1.
  Nat Struct Mol Biol, 13, 626-632.
PDB code: 2h94
16956976 Y.Chen, Y.Yang, F.Wang, K.Wan, K.Yamane, Y.Zhang, and M.Lei (2006).
Crystal structure of human histone lysine-specific demethylase 1 (LSD1).
  Proc Natl Acad Sci U S A, 103, 13956-13961.
PDB code: 2hko
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 code is shown on the right.