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PDBsum entry 1yio

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protein metals links
DNA binding protein PDB id
1yio
Jmol
Contents
Protein chain
198 a.a. *
Metals
_MG
_HG ×3
Waters ×90
* Residue conservation analysis
PDB id:
1yio
Name: DNA binding protein
Title: Crystallographic structure of response regulator styr from pseudomonas fluorescens
Structure: Response regulatory protein. Chain: a. Synonym: response regulator styr. Engineered: yes
Source: Pseudomonas fluorescens. Organism_taxid: 294. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.20Å     R-factor:   0.205     R-free:   0.275
Authors: M.Milani,L.Leoni,G.Rampioni,E.Zennaro,P.Ascenzi,M.Bolognesi
Key ref:
M.Milani et al. (2005). An active-like structure in the unphosphorylated StyR response regulator suggests a phosphorylation- dependent allosteric activation mechanism. Structure, 13, 1289-1297. PubMed id: 16154086 DOI: 10.1016/j.str.2005.05.014
Date:
12-Jan-05     Release date:   27-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O30989  (O30989_PSEFL) -  Response regulatory protein
Seq:
Struc:
208 a.a.
198 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     intracellular signal transduction   4 terms 
  Biochemical function     two-component response regulator activity     4 terms  

 

 
DOI no: 10.1016/j.str.2005.05.014 Structure 13:1289-1297 (2005)
PubMed id: 16154086  
 
 
An active-like structure in the unphosphorylated StyR response regulator suggests a phosphorylation- dependent allosteric activation mechanism.
M.Milani, L.Leoni, G.Rampioni, E.Zennaro, P.Ascenzi, M.Bolognesi.
 
  ABSTRACT  
 
StyR belongs to the FixJ subfamily of signal transduction response regulators; it controls transcription of the styABCD operon coding for styrene catabolism in Pseudomonas fluorescens ST. The crystal structure of unphosphorylated StyR is reported at 2.2 A resolution. StyR is composed of an N-terminal regulatory domain (StyR-N) and a C-terminal DNA binding domain (StyR-C). The two domains are separated by an elongated linker alpha helix (34 residues), a new feature in known response regulator structures. StyR-C is structured similarly to the DNA binding domain of the response regulator NarL. StyR-N shows structural reorganization of the phosphate receiving region involved in activation/homodimerization: specific residues adopt an "active-like" conformation, and the alpha4 helix, involved in dimerization of the homologous FixJ response regulator, is trimmed to just one helical turn. Overall, structural considerations suggest that phosphorylation may act as an allosteric switch, shifting a preexisting StyR equilibrium toward the active, dimeric, DNA binding form.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Overall Fold of Unphosphorylated StyR
The StyR-N domain showing the (ba)[5] fold is depicted in yellow (b strands 1-5) and in blue (a helices 1-4). The phosphorylation site residues, together with Thr83 and Phe102, the residues transmitting phosphorylation effects on the protein surface, are indicated in ball and stick representation. The a5 helix, last in the StyR-N domain and continuously connected with the interdomain linker helix, is colored in red. In the StyR-C domain, the proposed DNA binding helix-turn-helix motif is shown in blue (a8 is the recognition helix), and the hypothetical C-terminal dimerization helix is shown in light brown. Water molecules are shown as red spheres; a purple sphere indicates the Mg2+ ion. The inset provides details of the coordination sphere around the Mg2+ ion; a carbonyl group provided by the backbone of residue Arg57, one of the two axial ligands in the Mg2+ coordinated octahedron, is shown as C=O only, for display purposes.
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1289-1297) copyright 2005.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
19126546 R.K.Carroll, X.Liao, L.K.Morgan, E.M.Cicirelli, Y.Li, W.Sheng, X.Feng, and L.J.Kenney (2009).
Structural and Functional Analysis of the C-terminal DNA Binding Domain of the Salmonella typhimurium SPI-2 Response Regulator SsrB.
  J Biol Chem, 284, 12008-12019.  
18547423 G.Rampioni, L.Leoni, B.Pietrangeli, and E.Zennaro (2008).
The interplay of StyR and IHF regulates substrate-dependent induction and carbon catabolite repression of styrene catabolism genes in Pseudomonas fluorescens ST.
  BMC Microbiol, 8, 92.  
18353359 G.Wisedchaisri, M.Wu, D.R.Sherman, and W.G.Hol (2008).
Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation.
  J Mol Biol, 378, 227-242.
PDB codes: 3c3w 3c57
  19052358 R.Schnell, D.Agren, and G.Schneider (2008).
1.9 A structure of the signal receiver domain of the putative response regulator NarL from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1096-1100.
PDB code: 3eul
17433693 R.Gao, T.R.Mack, and A.M.Stock (2007).
Bacterial response regulators: versatile regulatory strategies from common domains.
  Trends Biochem Sci, 32, 225-234.  
16823552 A.Mooney, P.G.Ward, and K.E.O'Connor (2006).
Microbial degradation of styrene: biochemistry, molecular genetics, and perspectives for biotechnological applications.
  Appl Microbiol Biotechnol, 72, 1.  
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 codes are shown on the right.