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PDBsum entry 2fbk

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protein metals Protein-protein interface(s) links
Transcription PDB id
2fbk
Jmol
Contents
Protein chains
156 a.a. *
Metals
_CL ×2
Waters ×187
* Residue conservation analysis
PDB id:
2fbk
Name: Transcription
Title: The crystal structure of hucr from deinococcus radiodurans
Structure: Transcriptional regulator, marr family. Chain: a, b. Engineered: yes
Source: Deinococcus radiodurans. Organism_taxid: 1299. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.239     R-free:   0.289
Authors: T.Bordelon,S.P.Wilkinson,A.Grove,M.E.Newcomer
Key ref:
T.Bordelon et al. (2006). The crystal structure of the transcriptional regulator HucR from Deinococcus radiodurans reveals a repressor preconfigured for DNA binding. J Mol Biol, 360, 168-177. PubMed id: 16750221 DOI: 10.1016/j.jmb.2006.05.005
Date:
09-Dec-05     Release date:   04-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9RV71  (Q9RV71_DEIRA) -  Transcriptional regulator, MarR family
Seq:
Struc:
181 a.a.
156 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1016/j.jmb.2006.05.005 J Mol Biol 360:168-177 (2006)
PubMed id: 16750221  
 
 
The crystal structure of the transcriptional regulator HucR from Deinococcus radiodurans reveals a repressor preconfigured for DNA binding.
T.Bordelon, S.P.Wilkinson, A.Grove, M.E.Newcomer.
 
  ABSTRACT  
 
We report here the 2.3 A resolution structure of the hypothetical uricase regulator (HucR) from Deinococcus radiodurans R1. HucR, a member of the MarR family of DNA-binding proteins, was previously shown to repress its own expression as well as that of a uricase, a repression that is alleviated both in vivo and in vitro upon binding uric acid, the substrate for uricase. As uric acid is a potent scavenger of reactive oxygen species, and as D. radiodurans is known for its remarkable resistance to DNA-damaging agents, these observations indicate a novel oxidative stress response mechanism. The crystal structure of HucR in the absence of ligand or DNA reveals a dimer in which the DNA recognition helices are preconfigured for DNA binding. This configuration of DNA-binding domains is achieved through an apparently stable dimer interface that, in contrast to what is observed in other MarR homologs for which structures have been determined, shows little conformational heterogeneity in the absence of ligand. An additional amino-terminal segment, absent from other MarR homologs, appears to brace the principal helix of the dimerization interface. However, although HucR is preconfigured for DNA binding, the presence of a stacked pair of symmetry-related histidine residues at a central pivot point in the dimer interface suggests a mechanism for a conformational change to attenuate DNA binding.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Superposition of HucR and OhrR structures. The DNA-bound structure of OhrR (1Z9C) is in magenta and HucR is in blue. The recognition helices are in lighter shades.
Figure 5.
Figure 5. A region of the 2F[o]-F[c] electron density map. The map is contoured at 1s. The region corresponds to the dimer interface and the stacking of symmetry-related His51 residues is apparent.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 360, 168-177) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21432936 I.C.Perera, and A.Grove (2011).
MarR homologs with urate-binding signature.
  Protein Sci, 20, 621-629.  
20730247 A.Grove (2010).
Urate-responsive MarR homologs from Burkholderia.
  Mol Biosyst, 6, 2133-2142.  
20095047 C.Andrésen, S.Jalal, D.Aili, Y.Wang, S.Islam, A.Jarl, B.Liedberg, B.Wretlind, L.G.Mårtensson, and M.Sunnerhagen (2010).
Critical biophysical properties in the Pseudomonas aeruginosa efflux gene regulator MexR are targeted by mutations conferring multidrug resistance.
  Protein Sci, 19, 680-692.  
20716550 I.C.Perera, and A.Grove (2010).
Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators.
  J Mol Cell Biol, 2, 243-254.  
20513431 K.J.McLaughlin, C.M.Strain-Damerell, K.Xie, D.Brekasis, A.S.Soares, M.S.Paget, and C.L.Kielkopf (2010).
Structural basis for NADH/NAD+ redox sensing by a Rex family repressor.
  Mol Cell, 38, 563-575.
PDB codes: 3ikt 3ikv 3il2
21062374 S.Reverchon, F.Van Gijsegem, G.Effantin, O.Zghidi-Abouzid, and W.Nasser (2010).
Systematic targeted mutagenesis of the MarR/SlyA family members of Dickeya dadantii 3937 reveals a role for MfbR in the modulation of virulence gene expression in response to acidic pH.
  Mol Microbiol, 78, 1018-1037.  
  19255465 C.E.Nichols, S.Sainsbury, J.Ren, T.S.Walter, A.Verma, D.K.Stammers, N.J.Saunders, and R.J.Owens (2009).
The structure of NMB1585, a MarR-family regulator from Neisseria meningitidis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 204-209.
PDB code: 3g3z
19129225 M.Kumaraswami, J.T.Schuman, S.M.Seo, G.W.Kaatz, and R.G.Brennan (2009).
Structural and biochemical characterization of MepR, a multidrug binding transcription regulator of the Staphylococcus aureus multidrug efflux pump MepA.
  Nucleic Acids Res, 37, 1211-1224.
PDB code: 3eco
19509310 T.Kumarevel, T.Tanaka, T.Umehara, and S.Yokoyama (2009).
ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.
  Nucleic Acids Res, 37, 4723-4735.
PDB codes: 3gez 3gf2 3gfi 3gfj 3gfl 3gfm
18812515 M.S.Wilke, M.Heller, A.L.Creagh, C.A.Haynes, L.P.McIntosh, K.Poole, and N.C.Strynadka (2008).
The crystal structure of MexR from Pseudomonas aeruginosa in complex with its antirepressor ArmR.
  Proc Natl Acad Sci U S A, 105, 14832-14837.
PDB code: 3ech
18042459 K.J.Newberry, M.Fuangthong, W.Panmanee, S.Mongkolsuk, and R.G.Brennan (2007).
Structural mechanism of organic hydroperoxide induction of the transcription regulator OhrR.
  Mol Cell, 28, 652-664.
PDB codes: 2pex 2pfb
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.