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PDBsum entry 1r8d

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protein dna_rna ligands Protein-protein interface(s) links
Transcription/DNA PDB id
1r8d
Jmol
Contents
Protein chains
109 a.a. *
DNA/RNA
Ligands
SO4 ×2
Waters ×36
* Residue conservation analysis
PDB id:
1r8d
Name: Transcription/DNA
Title: Crystal structure of mtan bound to DNA
Structure: 26-mer. Chain: c. Engineered: yes. 26-mer. Chain: d. Engineered: yes. Transcription activator mtan. Chain: a, b. Fragment: n-terminal truncation mutant of mta.
Source: Synthetic: yes. Bacillus subtilis. Organism_taxid: 1423. Gene: mta. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.70Å     R-factor:   0.234     R-free:   0.269
Authors: K.J.Newberry,R.G.Brennan
Key ref:
K.J.Newberry and R.G.Brennan (2004). The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus. J Biol Chem, 279, 20356-20362. PubMed id: 14985361 DOI: 10.1074/jbc.M400960200
Date:
23-Oct-03     Release date:   17-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P71039  (MTA_BACSU) -  HTH-type transcriptional activator mta
Seq:
Struc:
257 a.a.
109 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     1 term  

 

 
DOI no: 10.1074/jbc.M400960200 J Biol Chem 279:20356-20362 (2004)
PubMed id: 14985361  
 
 
The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus.
K.J.Newberry, R.G.Brennan.
 
  ABSTRACT  
 
Transcription regulators of the MerR family respond to myriad stress signals to activate sigma70/sigmaA-targeted genes, which contain suboptimal 19-bp spacers between their -35 and -10 promoter elements. The crystal structure of a BmrR-TPP(+)-DNA complex provided initial insight into the transcription activation mechanism of the MerR family, which involves base pair distortion, DNA undertwisting and shortening of the spacer, and realignment of the -35 and -10 boxes. Here, we describe the crystal structure of MerR family member MtaN bound to the mta promoter. Although the global DNA binding modes of MtaN and BmrR differ somewhat, homologous protein-DNA interactions are maintained. Moreover, despite their different sequences, the mta promoter conformation is essentially identical to that of the BmrR-TPP(+)-bound bmr promoter, indicating that this DNA distortion mechanism is common to the entire MerR family. Interestingly, DNA binding experiments reveal that the identity of the two central bases of the mta and bmr promoters, which are conserved as either a thymidine or an adenine in nearly all MerR promoters, is not important for DNA affinity. Comparison of the free and DNA-bound MtaN structures reveals that a conformational hinge, centered at residues N-terminal to the ubiquitous coiled coil, is key for mta promoter binding. Analysis of the structures of BmrR, CueR, and ZntR indicates that this hinge may be common to all MerR family members.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. Structural mechanism of transcription activation by the MerR family. a, superimposition of the MtaN-DNA and BmrRTPP+-DNA complexes. Helices 1 to 4 of one subunit from each dimer, but not W1, were overlaid. Yellow, BmrR; blue, MtaN. b, overlay of the MtaN-mta and BmrR-bmr promoter structures using all equivalent phosphate backbone groups. Blue, mta DNA; yellow, bmr DNA. c, close up of the superimposed mta and bmr promoters near base pair 1. Notice their nearly identical structures at the site of DNA distortion. Blue sticks, mta promoter DNA; yellow sticks, bmr promoter DNA.
Figure 5.
FIG. 5. Representative DNA binding isotherms. a, equilibrium binding isotherm of BmrR titrated into bmrT[1]A[2] DNA. To ensure equilibrium binding, 0.2 nM fluorescein-labeled DNA was used in this experiment. b, equilibrium binding isotherm of MtaN titrated into MtaN-mtaT[1']T[2'] DNA. To ensure equilibrium binding, 1 nM fluorescein-labeled DNA was used in this experiment. mP, millipolarization.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 20356-20362) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153861 S.K.Checa, and F.C.Soncini (2011).
Bacterial gold sensing and resistance.
  Biometals, 24, 419-427.  
19880603 B.Berger, D.Moine, R.Mansourian, and F.Arigoni (2010).
HspR mutations are naturally selected in Bifidobacterium longum when successive heat shock treatments are applied.
  J Bacteriol, 192, 256-263.  
20580544 H.Wade (2010).
MD recognition by MDR gene regulators.
  Curr Opin Struct Biol, 20, 489-496.  
20230832 M.Kumaraswami, K.J.Newberry, and R.G.Brennan (2010).
Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR.
  J Mol Biol, 398, 264-275.
PDB code: 3iao
20442963 P.Chen, N.M.Andoy, J.J.Benítez, A.M.Keller, D.Panda, and F.Gao (2010).
Tackling metal regulation and transport at the single-molecule level.
  Nat Prod Rep, 27, 757-767.  
19507257 C.H.Wu, D.Le, A.Mulchandani, and W.Chen (2009).
Optimization of a whole-cell cadmium sensor with a toggle gene circuit.
  Biotechnol Prog, 25, 898-903.  
19651042 N.M.Andoy, S.K.Sarkar, Q.Wang, D.Panda, J.J.Benítez, A.Kalininskiy, and P.Chen (2009).
Single-molecule study of metalloregulator CueR-DNA interactions using engineered Holliday junctions.
  Biophys J, 97, 844-852.  
18316718 A.A.Gorodetsky, L.E.Dietrich, P.E.Lee, B.Demple, D.K.Newman, and J.K.Barton (2008).
DNA binding shifts the redox potential of the transcription factor SoxR.
  Proc Natl Acad Sci U S A, 105, 3684-3689.  
18593213 J.Zhao, W.Niu, J.Yao, S.Mohr, E.M.Marcotte, and A.M.Lambowitz (2008).
Group II intron protein localization and insertion sites are affected by polyphosphate.
  PLoS Biol, 6, e150.  
18658145 K.J.Newberry, J.L.Huffman, M.C.Miller, N.Vazquez-Laslop, A.A.Neyfakh, and R.G.Brennan (2008).
Structures of BmrR-drug complexes reveal a rigid multidrug binding pocket and transcription activation through tyrosine expulsion.
  J Biol Chem, 283, 26795-26804.
PDB codes: 3d6y 3d6z 3d70 3d71
18485073 S.A.Shelburne, D.B.Keith, M.T.Davenport, N.Horstmann, R.G.Brennan, and J.M.Musser (2008).
Molecular characterization of group A Streptococcus maltodextrin catabolism and its role in pharyngitis.
  Mol Microbiol, 69, 436-452.  
18334645 S.Watanabe, A.Kita, K.Kobayashi, and K.Miki (2008).
Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA.
  Proc Natl Acad Sci U S A, 105, 4121-4126.
PDB codes: 2zhg 2zhh
17233828 G.Navarro-Avilés, M.A.Jiménez, M.C.Pérez-Marín, C.González, M.Rico, F.J.Murillo, M.Elías-Arnanz, and S.Padmanabhan (2007).
Structural basis for operator and antirepressor recognition by Myxococcus xanthus CarA repressor.
  Mol Microbiol, 63, 980-994.
PDB code: 2jml
17085574 L.V.Wray, and S.H.Fisher (2007).
Functional analysis of the carboxy-terminal region of Bacillus subtilis TnrA, a MerR family protein.
  J Bacteriol, 189, 20-27.  
17367290 O.N.Oktyabrsky, and G.V.Smirnova (2007).
Redox regulation of cellular functions.
  Biochemistry (Mosc), 72, 132-145.  
17880214 S.K.Sarkar, N.M.Andoy, J.J.Benítez, P.R.Chen, J.S.Kong, C.He, and P.Chen (2007).
Engineered holliday junctions as single-molecule reporters for protein-DNA interactions with application to a MerR-family regulator.
  J Am Chem Soc, 129, 12461-12467.  
16547045 J.M.Zalieckas, L.V.Wray, and S.H.Fisher (2006).
Cross-regulation of the Bacillus subtilis glnRA and tnrA genes provides evidence for DNA binding site discrimination by GlnR and TnrA.
  J Bacteriol, 188, 2578-2585.  
16958847 J.Qiu, D.Zhou, L.Qin, Y.Han, X.Wang, Z.DU, Y.Song, and R.Yang (2006).
Microarray expression profiling of Yersinia pestis in response to chloramphenicol.
  FEMS Microbiol Lett, 263, 26-31.  
16911042 M.Ventura, C.Canchaya, Z.Zhang, V.Bernini, G.F.Fitzgerald, and D.van Sinderen (2006).
How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators.
  FEMS Microbiol Rev, 30, 734-759.  
  17142916 S.Watanabe, A.Kita, K.Kobayashi, Y.Takahashi, and K.Miki (2006).
Crystallization and preliminary X-ray crystallographic studies of the oxidative-stress sensor SoxR and its complex with DNA.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1275-1277.  
15629942 A.C.Hunt, L.Servín-González, G.H.Kelemen, and M.J.Buttner (2005).
The bldC developmental locus of Streptomyces coelicolor encodes a member of a family of small DNA-binding proteins related to the DNA-binding domains of the MerR family.
  J Bacteriol, 187, 716-728.  
16158235 J.L.Hobman, J.Wilkie, and N.L.Brown (2005).
A design for life: prokaryotic metal-binding MerR family regulators.
  Biometals, 18, 429-436.  
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 code is shown on the right.