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PDBsum entry 2p4w

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protein ligands Protein-protein interface(s) links
Transcription PDB id
2p4w
Jmol
Contents
Protein chains
197 a.a. *
Ligands
SO4
Waters ×47
* Residue conservation analysis
PDB id:
2p4w
Name: Transcription
Title: Crystal structure of heat shock regulator from pyrococcus fu
Structure: Transcriptional regulatory protein arsr family. Chain: a, b. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Gene: pf1790. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.60Å     R-factor:   0.255     R-free:   0.305
Authors: W.Liu,G.Vierke,S.Panjikar,M.Thomm,R.Ladenstein
Key ref:
W.Liu et al. (2007). Crystal Structure of the Archaeal Heat Shock Regulator from Pyrococcus furiosus: A Molecular Chimera Representing Eukaryal and Bacterial Features. J Mol Biol, 369, 474-488. PubMed id: 17434531 DOI: 10.1016/j.jmb.2007.03.044
Date:
13-Mar-07     Release date:   27-Mar-07    
Supersedes: 1xnp
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8U030  (Q8U030_PYRFU) -  Transcriptional regulatory protein arsR family
Seq:
Struc:
202 a.a.
197 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1016/j.jmb.2007.03.044 J Mol Biol 369:474-488 (2007)
PubMed id: 17434531  
 
 
Crystal Structure of the Archaeal Heat Shock Regulator from Pyrococcus furiosus: A Molecular Chimera Representing Eukaryal and Bacterial Features.
W.Liu, G.Vierke, A.K.Wenke, M.Thomm, R.Ladenstein.
 
  ABSTRACT  
 
We report here the crystal structure of a protein from Pyrococcus furiosus (Phr) that represents the first characterized heat shock transcription factor in archaea. Phr specifically represses the expression of heat shock genes at physiological temperature in vitro and in vivo but is released from the promoters upon heat shock response. Structure analysis revealed a stable homodimer, each subunit consisting of an N-terminal winged helix DNA-binding domain (wH-DBD) and a C-terminal antiparallel coiled coil helical domain. The overall structure shows as a molecular chimera with significant folding similarity of its DBD to the bacterial SmtB/ArsR family, while its C-terminal part was found to be a remote homologue of the eukaryotic BAG domain. The dimeric protein recognizes a palindromic DNA sequence. Molecular docking and mutational analyses suggested a novel binding mode in which the major specific contacts occur at the minor groove interacting with the strongly basic wing containing a cluster of three arginine residues.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Ribbon model of Phr. (a) Subunit structure; α-Helices, β-strands, loops shown in red, yellow and green, respectively. Cartoon model of a Phr dimer, (b) side view and (c) top view; chains rendered in blue and green; local 2-fold axes are indicated.
Figure 4.
Figure 4. Sequence and topology comparison between Phr C-terminal domain and human BAG domain (1HX1_B).^35 (a) Sequence alignment between the two domains, identical and similar amino acids shown in green and yellow, respectively; structure elements drawn according to Figure 1. (b) Structure comparison between Phr (left) and human BAG domain (right).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 369, 474-488) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20023014 A.M.Keese, G.J.Schut, M.Ouhammouch, M.W.Adams, and M.Thomm (2010).
Genome-wide identification of targets for the archaeal heat shock regulator phr by cell-free transcription of genomic DNA.
  J Bacteriol, 192, 1292-1298.  
20565873 C.C.Chou, M.Rajasekaran, and C.Chen (2010).
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking.
  BMC Bioinformatics, 11, 334.  
20598080 H.Yang, G.L.Lipscomb, A.M.Keese, G.J.Schut, M.Thomm, M.W.Adams, B.C.Wang, and R.A.Scott (2010).
SurR regulates hydrogen production in Pyrococcus furiosus by a sulfur-dependent redox switch.
  Mol Microbiol, 77, 1111-1122.  
20466807 M.van Dijk, and A.M.Bonvin (2010).
Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.
  Nucleic Acids Res, 38, 5634-5647.  
19887527 T.Kanai, S.Takedomi, S.Fujiwara, H.Atomi, and T.Imanaka (2010).
Identification of the Phr-dependent heat shock regulon in the hyperthermophilic archaeon, Thermococcus kodakaraensis.
  J Biochem, 147, 361-370.  
19554260 B.Klinkert, and F.Narberhaus (2009).
Microbial thermosensors.
  Cell Mol Life Sci, 66, 2661-2676.  
18390887 Q.Lu, J.Han, L.Zhou, J.A.Coker, P.DasSarma, S.DasSarma, and H.Xiang (2008).
Dissection of the regulatory mechanism of a heat-shock responsive promoter in Haloarchaea: a new paradigm for general transcription factor directed archaeal gene regulation.
  Nucleic Acids Res, 36, 3031-3042.  
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.