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PDBsum entry 1utb
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protein ligands Protein-protein interface(s) links
Transcription regulation PDB id
1utb

 

 

 

 

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Contents
Protein chains
214 a.a. *
227 a.a. *
Ligands
GOL ×5
ACT ×2
Waters ×113
* Residue conservation analysis
PDB id:
1utb
Name: Transcription regulation
Title: Dntr from burkholderia sp. Strain dnt
Structure: Lysr-type regulatory protein. Chain: a. Engineered: yes. Mutation: yes. Lysr-type regulatory protein. Chain: b. Engineered: yes. Mutation: yes
Source: Burkholderia sp.. Organism_taxid: 233098. Strain: dnt. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
2.59Å     R-factor:   0.217     R-free:   0.261
Authors: I.A.Smirnova,C.Dian,G.A.Leonard,S.Mcsweeney,D.Birse,P.Brzezinski
Key ref:
I.A.Smirnova et al. (2004). Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator DntR. J Mol Biol, 340, 405-418. PubMed id: 15210343 DOI: 10.1016/j.jmb.2004.04.071
Date:
05-Dec-03     Release date:   01-Jul-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7WT50  (Q7WT50_9BURK) -  LysR-type regulatory protein from Burkholderia sp. DNT
Seq:
Struc: 		301 a.a.
214 a.a.*
Protein chain
Pfam   ArchSchema ?
Q7WT50  (Q7WT50_9BURK) -  LysR-type regulatory protein from Burkholderia sp. DNT
Seq:
Struc: 		301 a.a.
227 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.jmb.2004.04.071 J Mol Biol 340:405-418 (2004)
PubMed id: 15210343  
 
 
Development of a bacterial biosensor for nitrotoluenes: the crystal structure of the transcriptional regulator DntR.
I.A.Smirnova, C.Dian, G.A.Leonard, S.McSweeney, D.Birse, P.Brzezinski.
 
  ABSTRACT  
 
The transcriptional regulator DntR, a member of the LysR family, is a central element in a prototype bacterial cell-based biosensor for the detection of hazardous contamination of soil and groundwater by dinitrotoluenes. To optimise the sensitivity of the biosensor for such compounds we have chosen a rational design of the inducer-binding cavity based on knowledge of the three-dimensional structure of DntR. We report two crystal structures of DntR with acetate (resolution 2.6 angstroms) and thiocyanate (resolution 2.3 angstroms), respectively, occupying the inducer-binding cavity. These structures allow for the construction of models of DntR in complex with salicylate (Kd approximately or = 4 microM) and 2,4-dinitrotoluene that provide a basis for the design of mutant DntR with enhanced specificity for dinitrotoluenes. In both crystal structures DntR crystallises as a homodimer with a "head-to-tail" arrangement of monomers in the asymmetric unit. Analysis of the crystal structure has allowed the building of a full-length model of DntR in its biologically active homotetrameric form consisting of two "head-to-head" dimers. The implications of this model for the mechanism of transcription regulation by LysR proteins are discussed.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. DntR–ligand interactions. Stereoviews showing substrate–protein interactions for the acetate-bound crystals (a) and for the models of DntR containing salicylate (b) and 2,4-DNT (c) in the inducer-binding cavities. The surface defined by protein residues is shown in light purple. Both side-chain and main-chain atoms of amino acid residues that line the inducer-binding cavity are shown in ball-and-stick representation with carbon atoms coloured grey, oxygen atoms red and nitrogen atoms blue. Acetate, salicylate and 2,4-DNT are also shown in ball-and-stick mode with carbon atoms coloured yellow, oxygen atoms red and nitrogen atoms blue. Water molecules are shown as red spheres. Direct and water-mediated hydrogen bonding interactions are shown as green and yellow broken lines, respectively. 		Figure 6.
Figure 6. The DntR homotetramer. (a) A ribbon representation of the homotetramer of DntR. The two molecules that make up the dimer in the asymmetric unit of the DntR crystals are shown in red and blue, respectively. The arrows indicate the position of the linker helices of the monomers B. The homotetramer is the result of the interaction of two homodimers related by a crystallographic symmetry such that the two dimers that constitute the homotetramer have co-ordinates (x, y, z) and (1−x, y, 1/2−z).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 340, 405-418) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205010 A.de Las Heras, and V.de Lorenzo (2011).
Cooperative amino acid changes shift the response of the σ(54) -dependent regulator XylR from natural m-xylene towards xenobiotic 2,4-dinitrotoluene.
  Mol Microbiol, 79, 1248-1259.  
21362064 G.S.Joshi, C.E.Bobst, and F.R.Tabita (2011).
Unravelling the regulatory twist - regulation of CO(2) fixation in Rhodopseudomonas palustris CGA010 mediated by atypical response regulator(s)(†).
  Mol Microbiol, 80, 756-771.  
21187915 G.S.Knapp, and J.C.Hu (2010).
Specificity of the E. coli LysR-type transcriptional regulators.
  PLoS One, 5, e15189.  
20478059 S.Sainsbury, J.Ren, J.E.Nettleship, N.J.Saunders, D.I.Stuart, and R.J.Owens (2010).
The structure of a reduced form of OxyR from Neisseria meningitidis.
  BMC Struct Biol, 10, 10.
PDB code: 3jv9
19779647 B.Hou, F.Li, X.Yang, and G.Hong (2009).
A small functional intramolecular region of NodD was identified by mutation.
  Acta Biochim Biophys Sin (Shanghai), 41, 822-830.  
19319522 G.H.Lang, and N.Ogawa (2009).
Mutational analysis of the inducer recognition sites of the LysR-type transcriptional regulator TfdT of Burkholderia sp. NK8.
  Appl Microbiol Biotechnol, 83, 1085-1094.  
19760662 G.S.Knapp, and J.C.Hu (2009).
The oligomerization of CynR in Escherichia coli.
  Protein Sci, 18, 2307-2315.  
19177355 G.S.Knapp, J.W.Tsai, and J.C.Hu (2009).
The oligomerization of OxyR in Escherichia coli.
  Protein Sci, 18, 101-107.  
19400783 S.H.Craven, O.C.Ezezika, S.Haddad, R.A.Hall, C.Momany, and E.L.Neidle (2009).
Inducer responses of BenM, a LysR-type transcriptional regulator from Acinetobacter baylyi ADP1.
  Mol Microbiol, 72, 881-894.
PDB codes: 2h99 2h9b 3glb
19474343 S.Sainsbury, L.A.Lane, J.Ren, R.J.Gilbert, N.J.Saunders, C.V.Robinson, D.I.Stuart, and R.J.Owens (2009).
The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators.
  Nucleic Acids Res, 37, 4545-4558.
PDB codes: 3hhf 3hhg
  18678953 D.Monferrer, T.Tralau, M.A.Kertesz, S.Panjikar, and I.Usón (2008).
High crystallizability under air-exclusion conditions of the full-length LysR-type transcriptional regulator TsaR from Comamonas testosteroni T-2 and data-set analysis for a MIRAS structure-solution approach.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 764-769.  
19047729 S.E.Maddocks, and P.C.Oyston (2008).
Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins.
  Microbiology, 154, 3609-3623.  
  18765907 S.Sainsbury, J.Ren, N.J.Saunders, D.I.Stuart, and R.J.Owens (2008).
Crystallization and preliminary X-ray analysis of CrgA, a LysR-type transcriptional regulator from pathogenic Neisseria meningitidis MC58.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 797-801.  
  17565172 O.C.Ezezika, S.Haddad, E.L.Neidle, and C.Momany (2007).
Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 361-368.
PDB codes: 2f8d 2f97
17134717 S.Picossi, B.R.Belitsky, and A.L.Sonenshein (2007).
Molecular mechanism of the regulation of Bacillus subtilis gltAB expression by GltC.
  J Mol Biol, 365, 1298-1313.  
16855231 M.C.Peck, R.F.Fisher, and S.R.Long (2006).
Diverse flavonoids stimulate NodD1 binding to nod gene promoters in Sinorhizobium meliloti.
  J Bacteriol, 188, 5417-5427.  
16446453 S.van Sint Fiet, J.B.van Beilen, and B.Witholt (2006).
Selection of biocatalysts for chemical synthesis.
  Proc Natl Acad Sci U S A, 103, 1693-1698.  
16359854 T.C.Galvão, and V.de Lorenzo (2006).
Transcriptional regulators à la carte: engineering new effector specificities in bacterial regulatory proteins.
  Curr Opin Biotechnol, 17, 34-42.  
15755957 A.Brencic, and S.C.Winans (2005).
Detection of and response to signals involved in host-microbe interactions by plant-associated bacteria.
  Microbiol Mol Biol Rev, 69, 155-194.  
16102008 A.W.Dangel, J.L.Gibson, A.P.Janssen, and F.R.Tabita (2005).
Residues that influence in vivo and in vitro CbbR function in Rhodobacter sphaeroides and identification of a specific region critical for co-inducer recognition.
  Mol Microbiol, 57, 1397-1414.  
15546870 M.C.Justino, J.B.Vicente, M.Teixeira, and L.M.Saraiva (2005).
New genes implicated in the protection of anaerobically grown Escherichia coli against nitric oxide.
  J Biol Chem, 280, 2636-2643.  
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.

 

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