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PDBsum entry 3coq
Go to PDB code: 
protein dna_rna ligands metals Protein-protein interface(s) links
Transcription/DNA PDB id
3coq

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
89 a.a. *
DNA/RNA
Ligands
MPD
Metals
_ZN ×4
Waters ×33
* Residue conservation analysis
PDB id:
3coq
Name: Transcription/DNA
Title: Structural basis for dimerization in DNA recognition by gal4
Structure: DNA (5'- d( Dap Dcp Dcp Dgp Dgp Dap Dgp Dgp Dap Dcp Dap Dgp Dtp Dcp Dcp Dtp Dc p Dcp Dgp Dg)-3'). Chain: d. Engineered: yes. DNA (5'- d( Dtp Dcp Dcp Dgp Dgp Dap Dgp Dgp Dap Dcp Dtp Dgp Dtp Dcp Dcp Dtp Dc p Dcp Dgp Dg)-3'). Chain: e.
Source: Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: gal4. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.213     R-free:   0.269
Authors: M.Hong,M.X.Fitzgerald,S.Harper,C.Luo,D.W.Speicher
Key ref: M.Hong et al. (2008). Structural basis for dimerization in DNA recognition by Gal4. Structure, 16, 1019-1026. PubMed id: 18611375
Date:
29-Mar-08     Release date:   01-Jul-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04386  (GAL4_YEAST) -  Regulatory protein GAL4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		881 a.a.
89 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  A-C-C-G-G-A-G-G-A-C-A-G-T-C-C-T-C-C-G-G 20 bases
  T-C-C-G-G-A-G-G-A-C-T-G-T-C-C-T-C-C-G-G 20 bases

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Structure 16:1019-1026 (2008)
PubMed id: 18611375  
 
 
Structural basis for dimerization in DNA recognition by Gal4.
M.Hong, M.X.Fitzgerald, S.Harper, C.Luo, D.W.Speicher, R.Marmorstein.
 
  ABSTRACT  
 
Gal4 is a Zn2Cys6 binuclear cluster containing transcription factor that binds DNA as a homodimer and can activate transcription by interacting with the mutant Gal11P protein. Although structures have been reported of the Gal4 dimerization domain and the binuclear cluster domain bound to DNA as a dimer, the structure of the "complete" Gal4 dimer bound to DNA has not previously been described. Here we report the structure of a complete Gal4 dimer bound to DNA and additional biochemical studies to address the molecular basis for Gal4 dimerization in DNA binding. We find that Gal4 dimerization on DNA is mediated by an intertwined helical bundle that deviates significantly from the solution NMR structure of the free dimerization domain. Associated biochemical studies show that the dimerization domain of Gal4 is important for DNA binding and protein thermostability. We also map the interaction surface of the Gal4 dimerization domain with Gal11P.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20953181 M.D.Daugherty, B.Liu, and A.D.Frankel (2010).
Structural basis for cooperative RNA binding and export complex assembly by HIV Rev.
  Nat Struct Mol Biol, 17, 1337-1342.
PDB code: 3lph
20434983 M.Floer, X.Wang, V.Prabhu, G.Berrozpe, S.Narayan, D.Spagna, D.Alvarez, J.Kendall, A.Krasnitz, A.Stepansky, J.Hicks, G.O.Bryant, and M.Ptashne (2010).
A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding.
  Cell, 141, 407-418.  
19380488 H.Murakami, and A.Nicolas (2009).
Locally, meiotic double-strand breaks targeted by Gal4BD-Spo11 occur at discrete sites with a sequence preference.
  Mol Cell Biol, 29, 3500-3516.  
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.

 

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