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PDBsum entry 1fym

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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
1fym
Jmol
Contents
Protein chains
86 a.a. *
78 a.a. *
DNA/RNA
Waters ×92
* Residue conservation analysis
PDB id:
1fym
Name: Transcription/DNA
Title: Serendipitous crystal structure containing the heat shock transcription factor's DNA binding domain and cognate DNA in a tail-to-tail orientation
Structure: Tail-to-tail hse. Chain: c, d. Engineered: yes. Heat shock transcription protein. Chain: a, b. Fragment: DNA binding domain. Synonym: heat shock transcription factor. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Other_details: this sequence is based on an idealized hse sequence.. Kluyveromyces lactis. Organism_taxid: 28985. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.211     R-free:   0.295
Authors: O.Littlefield,H.C.M.Nelson
Key ref:
O.Littlefield and H.C.Nelson (2001). Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex. Proteins, 45, 219-228. PubMed id: 11599025 DOI: 10.1002/prot.1142
Date:
02-Oct-00     Release date:   28-Sep-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22121  (HSF_KLULA) -  Heat shock factor protein
Seq:
Struc:
 
Seq:
Struc:
677 a.a.
86 a.a.*
Protein chain
Pfam   ArchSchema ?
P22121  (HSF_KLULA) -  Heat shock factor protein
Seq:
Struc:
 
Seq:
Struc:
677 a.a.
78 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     sequence-specific DNA binding transcription factor activity     2 terms  

 

 
DOI no: 10.1002/prot.1142 Proteins 45:219-228 (2001)
PubMed id: 11599025  
 
 
Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex.
O.Littlefield, H.C.Nelson.
 
  ABSTRACT  
 
We present here three high-resolution crystal structures of complexes between the DNA-binding domain of the heat-shock transcription factor (HSF) and DNA oligomers. Although the DNA oligomers contain HSF's specific binding sequence, called a heat-shock element, the crystal structures do not contain the specific protein-DNA complex. In one crystal structure, the 10 base pair DNA oligomer is statically disordered. In the other two related structures, the 12 base pair DNA oligomers are in unique positions, but the protein-DNA contacts in these two crystals are not sequence specific. In all three structures, the DNA appears to act as a rigid, polyanion scaffold to support columns of proteins in a crystalline lattice. A robust crystal packing interface between protein monomers obscures the true DNA-binding surface, known from previous genetic and biochemical studies. By redesigning the protein to interfere with the crystal lattice contacts, we were able to obtain physiologically relevant crystals in a specific protein-DNA complex. Thus, a crystal-packing interface was able to prevent the weak, but physiological relevant interactions between a protein and DNA.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Overlap of the DNAs from the HtH and TtT structures aligned by superimposing the phosphates in the program O.[19] The HtH DNAs are colored red; the r.m.s.d. for alignment of the phosphates is 1.26 Å. The TtT DNAs are colored blue; the r.m.s.d. for alignment of the phosphates is 1.27 Å. A: Superposition of the C DNAs; the r.m.s.d. for alignment of the phosphates is 0.61 Å. B: Superposition of the D DNAs; the r.m.s.d. for the alignment of the phosphates is 0.72.
Figure 6.
Figure 6. Two views of four different protein-DNA complexes. A,B: Interactions between HtH protein A and DNA. C,D: Interactions between HtH protein B and DNA. E,F: Interactions between the HSF DNA-binding domain specific complex and DNA[14] (PDB coordinates ). G,H: Interactions between the engineered Cro monomer and DNA[30] (PDB coordinates 3ORC). The interactions between TtT and proteins A and B are similar to that seen for the HtH structure. The DNA is colored yellow and the protein is cyan with the recognition helix highlighted in red. The views in the left-hand column (a, c, e, and g) are down the recognition helix axis.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2001, 45, 219-228) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16452152 K.W.Park, J.S.Hahn, Q.Fan, D.J.Thiele, and L.Li (2006).
De novo appearance and "strain" formation of yeast prion [PSI+] are regulated by the heat-shock transcription factor.
  Genetics, 173, 35-47.  
14997553 Z.Kovári, and M.Vas (2004).
Protein conformer selection by sequence-dependent packing contacts in crystals of 3-phosphoglycerate kinase.
  Proteins, 55, 198-209.  
12235156 F.Guo, L.Esser, S.K.Singh, M.R.Maurizi, and D.Xia (2002).
Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA.
  J Biol Chem, 277, 46753-46762.
PDB codes: 1mbu 1mbv 1mbx
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