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PDBsum entry 1mi7

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Transcription PDB id
1mi7
Jmol
Contents
Protein chain
103 a.a. *
Ligands
IPA
Waters ×47
* Residue conservation analysis
PDB id:
1mi7
Name: Transcription
Title: Crystal structure of domain swapped trp aporepressor in 30%( isopropanol
Structure: Trp operon repressor. Chain: r. Engineered: yes. Other_details: aporepressor
Source: Escherichia coli. Organism_taxid: 562. Gene: trpr. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.255     R-free:   0.288
Authors: C.L.Lawson,B.Benoff,T.Berger,H.M.Berman,J.Carey
Key ref:
C.L.Lawson et al. (2004). E. coli trp repressor forms a domain-swapped array in aqueous alcohol. Structure, 12, 1099-1108. PubMed id: 15274929 DOI: 10.1016/j.str.2004.03.019
Date:
22-Aug-02     Release date:   02-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A881  (TRPR_ECOLI) -  Trp operon repressor
Seq:
Struc:
108 a.a.
103 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     transcription, DNA-dependent   3 terms 
  Biochemical function     DNA binding     3 terms  

 

 
DOI no: 10.1016/j.str.2004.03.019 Structure 12:1099-1108 (2004)
PubMed id: 15274929  
 
 
E. coli trp repressor forms a domain-swapped array in aqueous alcohol.
C.L.Lawson, B.Benoff, T.Berger, H.M.Berman, J.Carey.
 
  ABSTRACT  
 
The E. coli trp repressor (trpR) homodimer recognizes its palindromic DNA binding site through a pair of flexible helix-turn-helix (HTH) motifs displayed on an intertwined helical core. Flexible N-terminal arms mediate association between dimers bound to tandem DNA sites. The 2.5 A X-ray structure of trpR crystallized in 30% (v/v) isopropanol reveals a substantial conformational rearrangement of HTH motifs and N-terminal arms, with the protein appearing in the unusual form of an ordered 3D domain-swapped supramolecular array. Small angle X-ray scattering measurements show that the self-association properties of trpR in solution are fundamentally altered by isopropanol.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Domain-Swapped trpR(A) Electron density derived from initial molecular replacement phases. "Solvent-flipped" map (Abrahams and Leslie, 1996) is shown overlaid on Ca traces of several crystal-symmetry equivalent subunits of the dimer molecular replacement search model (varied colors). Residues Leu62 (cyan subunit) and Ile79 (green subunit) define the boundaries of a helical span of density between crystallographically related copies of the search model. Search model D helices sit outside of electron density.(B) The ds-trpR array hexagonal crystal lattice, ab plane view. All protein atoms within one unit cell c repeat are shown. The polypeptide backbone path of a single trpR subunit, representing one asymmetric unit of the P6[1]22 symmetry structure, is represented with a cyan ribbon. Pores within the lattice are vert, similar 50 in diameter (gray arrow in pore indicates view orientation of [A]).(C) Domain-swapped trpR, schematic ribbon view. The central cyan subunit, shown in same orientation as cyan subunit in (B), bridges two "nodes" of the array. Truncated segments of equivalent subunits that complete the two nodes are shown in alternating colors, with positions of truncation indicated by orange circles. The orientation of the upper left node is equivalent to the orientation of the trpR dimer in Figure 1A. Helices of the cyan subunit are labeled according to dimer convention. Helices C-E of the dimer coalesce to form a long, central helix in ds-trpR.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1099-1108) copyright 2004.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17601995 C.Yanofsky (2007).
RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria.
  RNA, 13, 1141-1154.  
17962398 J.Carey, S.Lindman, M.Bauer, and S.Linse (2007).
Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency.
  Protein Sci, 16, 2317-2333.  
16698543 M.J.Bennett, M.R.Sawaya, and D.Eisenberg (2006).
Deposition diseases and 3D domain swapping.
  Structure, 14, 811-824.  
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