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PDBsum entry 3bpx

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protein ligands metals Protein-protein interface(s) links
Transcription regulator PDB id
3bpx
Jmol
Contents
Protein chains
147 a.a. *
138 a.a. *
Ligands
SAL ×2
Metals
_NA ×6
Waters ×244
* Residue conservation analysis
PDB id:
3bpx
Name: Transcription regulator
Title: Crystal structure of marr
Structure: Transcriptional regulator. Chain: a, b. Engineered: yes
Source: Methanobacterium thermoautotrophicum. Gene: mt313. Expressed in: escherichia coli.
Resolution:
1.95Å     R-factor:   0.222     R-free:   0.284
Authors: V.Saridakis,D.Shahinas,X.Xu,D.Christendat
Key ref:
V.Saridakis et al. (2008). Structural insight on the mechanism of regulation of the MarR family of proteins: high-resolution crystal structure of a transcriptional repressor from Methanobacterium thermoautotrophicum. J Mol Biol, 377, 655-667. PubMed id: 18272181 DOI: 10.1016/j.jmb.2008.01.001
Date:
19-Dec-07     Release date:   20-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O26413  (O26413_METTH) -  Transcriptional regulator
Seq:
Struc:
146 a.a.
147 a.a.
Protein chain
Pfam   ArchSchema ?
O26413  (O26413_METTH) -  Transcriptional regulator
Seq:
Struc:
146 a.a.
138 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     3 terms  

 

 
DOI no: 10.1016/j.jmb.2008.01.001 J Mol Biol 377:655-667 (2008)
PubMed id: 18272181  
 
 
Structural insight on the mechanism of regulation of the MarR family of proteins: high-resolution crystal structure of a transcriptional repressor from Methanobacterium thermoautotrophicum.
V.Saridakis, D.Shahinas, X.Xu, D.Christendat.
 
  ABSTRACT  
 
Transcriptional regulators belonging to the MarR family are characterized by a winged-helix DNA binding domain. These transcriptional regulators regulate the efflux and influx of phenolic agents in bacteria and archaea. In Escherichia coli, MarR regulates the multiple antibiotic resistance operon and its inactivation produces a multiple antibiotic resistance phenotype. In some organisms, active efflux of drug compounds will produce a drug resistance phenotype, whereas in other organisms, active influx of chlorinated hydrocarbons results in their rapid degradation. Although proteins in the MarR family are regulators of important biological processes, their mechanism of action is not well understood and structural information about how phenolic agents regulate the activity of these proteins is lacking. This article presents the three-dimensional structure of a protein of the MarR family, MTH313, in its apo form and in complex with salicylate, a known inactivator. A comparison of these two structures indicates that the mechanism of regulation involves a large conformational change in the DNA binding lobe. Electrophoretic mobility shift assay and biophysical analyses further suggest that salicylate inactivates MTH313 and prevents it from binding to its promoter region.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Comparison of the top DALI structural homologues at the helix–turn–helix motif reveals conservation of the ligand binding pocket in three-dimensional space. (a) Structure-based alignment of the top DALI structural homologues. (b) The identified salicylate binding site of M. thermoautotrophicum consists mainly of basic and hydrophobic residues. (c) E. faecalis SlyA (PDB ID: 1LJ9) is the closest structural homologue to MTH313. The binding site contains similar composition of hydrophobic and basic residues. (d) In B. subtilis OhrR (PDB ID: 1Z91), the redox cysteine, residue 15, is identified in the binding pocket (substituted to Ser15 in the coordinate file). (e) The identified binding site in E. coli MarR (1JGS). (f) The identified binding site for EmrR from S. tokodaii (2GXG). The identified binding site contains a high proportion of polar and charged residues.
Figure 3.
Fig. 3. (a) Electrostatic surface representation of MTH313 in the apo and in complex with salicylate. The arrow is pointing at the first binding site. The identified binding pocket consists of a high proportion of basic residues, which may indicate its potential to bind different ligands. (b) Electrostatic representation of the two salicylate binding sites in the dimer. (c) A representation of some of the binding site residues relative to the bound salicylate in the binding pocket. In the first binding site (SAL1), salicylate made distinct interactions with both Arg16 and Lys8. The electron density for the bound salicylates was obtained from a 2F[o] − F[c] composite omit map.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 377, 655-667) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19585113 L.Horbal, Y.Rebets, M.Rabyk, A.Luzhetskyy, B.Ostash, E.Welle, T.Nakamura, V.Fedorenko, and A.Bechthold (2010).
Characterization and analysis of the regulatory network involved in control of lipomycin biosynthesis in Streptomyces aureofaciens Tü117.
  Appl Microbiol Biotechnol, 85, 1069-1079.  
20421503 Y.M.Chang, W.Y.Jeng, T.P.Ko, Y.J.Yeh, C.K.Chen, and A.H.Wang (2010).
Structural study of TcaR and its complexes with multiple antibiotics from Staphylococcus epidermidis.
  Proc Natl Acad Sci U S A, 107, 8617-8622.
PDB codes: 3kp2 3kp3 3kp4 3kp5 3kp6 3kp7
19586910 C.B.Poor, P.R.Chen, E.Duguid, P.A.Rice, and C.He (2009).
Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus.
  J Biol Chem, 284, 23517-23524.
PDB codes: 3hrm 3hse 3hsr
  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
19129220 W.Eiamphungporn, S.Soonsanga, J.W.Lee, and J.D.Helmann (2009).
Oxidation of a single active site suffices for the functional inactivation of the dimeric Bacillus subtilis OhrR repressor in vitro.
  Nucleic Acids Res, 37, 1174-1181.  
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
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.