spacer
spacer

PDBsum entry 2jhe

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Transcription PDB id
2jhe
Jmol
Contents
Protein chains
189 a.a. *
Ligands
AE3
PG4 ×2
SO4
Waters ×146
* Residue conservation analysis
PDB id:
2jhe
Name: Transcription
Title: N-terminal domain of tyrr transcription factor (residues 1 - 190)
Structure: Transcription regulator tyrr. Chain: a, b, c, d. Fragment: n-terminal domain, residues 1-190. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.252     R-free:   0.317
Authors: D.Verger,P.D.Carr,T.Kwok,D.L.Ollis
Key ref:
D.Verger et al. (2007). Crystal structure of the N-terminal domain of the TyrR transcription factor responsible for gene regulation of aromatic amino acid biosynthesis and transport in Escherichia coli K12. J Mol Biol, 367, 102-112. PubMed id: 17222426 DOI: 10.1016/j.jmb.2006.12.018
Date:
21-Feb-07     Release date:   24-Jun-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07604  (TYRR_ECOLI) -  Transcriptional regulatory protein TyrR
Seq:
Struc:
513 a.a.
189 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     signal transducer activity     2 terms  

 

 
DOI no: 10.1016/j.jmb.2006.12.018 J Mol Biol 367:102-112 (2007)
PubMed id: 17222426  
 
 
Crystal structure of the N-terminal domain of the TyrR transcription factor responsible for gene regulation of aromatic amino acid biosynthesis and transport in Escherichia coli K12.
D.Verger, P.D.Carr, T.Kwok, D.L.Ollis.
 
  ABSTRACT  
 
The X-ray structure of the N-terminal domain of TyrR has been solved to a resolution of 2.3 A. It reveals a modular protein containing an ACT domain, a connecting helix, a PAS domain and a C-terminal helix. Two dimers are present in the asymmetric unit with one monomer of each pair exhibiting a large rigid-body movement that results in a hinging around residue 74 of approximately 50 degrees . The structure of the dimer is discussed with reference to other transcription regulator proteins. Putative binding sites are identified for the aromatic amino acid cofactors.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Selected views of a TyrR^NT dimer. (a) The view highlights the extension of the N-terminal ACT domains into a single eight-stranded sheet flanked on one side by antiparallel helices. (b) The view in (a) rotated around the NCS dyad relating the two N-terminal ACT domains. This view shows the rotation of the NCS dyad that relates the rest of the molecule to its dimer equivalent chain with respect to the first dyad. The B chain (blue) clearly shows four sub-domains; the N-terminal ACT domain, the connecting helix, the PAS domain, and the final C-terminal helix. (c) A topology diagram of a monomer of TyrR showing the separate domains. (d) The original view rotated 90° to look down on the N-terminal domains showing the twofold relationship between the monomers. (e) Looking from below at the C-terminal end of the molecule, the arrow indicates the direction of the view, i.e. along the second NCS dyad axis relating the PAS domains and the C-terminal helices. (f) The same view with the final C-terminal helix removed from each chain to give a clearer view of the PAS domains and connecting helices. Figure 2. Selected views of a TyrR^NT dimer. (a) The view highlights the extension of the N-terminal ACT domains into a single eight-stranded sheet flanked on one side by antiparallel helices. (b) The view in (a) rotated around the NCS dyad relating the two N-terminal ACT domains. This view shows the rotation of the NCS dyad that relates the rest of the molecule to its dimer equivalent chain with respect to the first dyad. The B chain (blue) clearly shows four sub-domains; the N-terminal ACT domain, the connecting helix, the PAS domain, and the final C-terminal helix. (c) A topology diagram of a monomer of TyrR showing the separate domains. (d) The original view rotated 90° to look down on the N-terminal domains showing the twofold relationship between the monomers. (e) Looking from below at the C-terminal end of the molecule, the arrow indicates the direction of the view, i.e. along the second NCS dyad axis relating the PAS domains and the C-terminal helices. (f) The same view with the final C-terminal helix removed from each chain to give a clearer view of the PAS domains and connecting helices.
Figure 3.
Figure 3. Overlay of the individual monomers of TyrR^NT. The N-terminal domains (residues 1–68) were superimposed. (left) A and B overlaid to show the conformational differences between monomers of the same dimer. (centre) A and C overlaid to show similarity of equivalent domains between dimers. (right) All four chains overlaid to show the full range of rigid body displacements. Figure 3. Overlay of the individual monomers of TyrR^NT. The N-terminal domains (residues 1–68) were superimposed. (left) A and B overlaid to show the conformational differences between monomers of the same dimer. (centre) A and C overlaid to show similarity of equivalent domains between dimers. (right) All four chains overlaid to show the full range of rigid body displacements.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 367, 102-112) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18931124 T.Koyanagi, T.Katayama, H.Suzuki, and H.Kumagai (2008).
Altered oligomerization properties of N316 mutants of Escherichia coli TyrR.
  J Bacteriol, 190, 8238-8243.  
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.