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PDBsum entry 1osl

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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
1osl
Jmol
Contents
Protein chains
62 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1osl
Name: Transcription/DNA
Title: Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence
Structure: Lactose operon repressor. Chain: a, b. Fragment: n-terminal DNA-binding domain, residues 1-62. Engineered: yes. Mutation: yes. 5'- d( Cp Gp Ap Tp Ap Ap Gp Ap Tp Ap Tp Cp Tp Tp Ap Tp Cp G)- 3'. Chain: c, d.
Source: Escherichia coli. Organism_taxid: 562. Gene: laci. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
NMR struc: 20 models
Authors: C.G.Kalodimos,A.M.J.J.Bonvin,R.Boelens,R.Kaptein
Key ref:
C.G.Kalodimos et al. (2004). Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science, 305, 386-389. PubMed id: 15256668 DOI: 10.1126/science.1097064
Date:
20-Mar-03     Release date:   04-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03023  (LACI_ECOLI) -  Lactose operon repressor
Seq:
Struc:
360 a.a.
62 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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

 

 
DOI no: 10.1126/science.1097064 Science 305:386-389 (2004)
PubMed id: 15256668  
 
 
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.
C.G.Kalodimos, N.Biris, A.M.Bonvin, M.M.Levandoski, M.Guennuegues, R.Boelens, R.Kaptein.
 
  ABSTRACT  
 
Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient finding of the target site.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Comparison of specific with nonspecific binding mode and interactions. In (A) and (B), the left sites of the specific O1 and nonspecific complexes are overlaid on their DNA backbone so that the protein position with respect to the DNA can be compared. The proteins in the specific and nonspecific complexes are colored yellow and red, respectively. (A) The protein in the nonspecific complex is rotated 25°, relative to the DNA, compared to the protein in the specific complex. In (B), the four most important residues for conferring specificity are shown and their conformation is compared. (C) Schematic summary of the protein-DNA contacts in the specific and nonspecific complex (25). The bases that are specifically recognized by lac repressor are colored yellow. The solid and dashed lines indicate interactions in the major and minor grooves, respectively. Red, green, and dashed blue lines indicate hydrogen bonding and hydrophobic and electrostatic contacts, respectively. (D) Salt concentration dependence of specific and nonspecific binding for wild-type (wt) and Y17F repressors.
Figure 3.
Fig. 3. Structural pathway of protein-DNA recognition. The hinge region (residues 50 to 62), which is colored red, remains unstructured in both the free state and the nonspecific complex, whereas it folds up to an helix in the specific complex with the natural operator O1. In the nonspecific complex, the DNA adopts a canonical B-DNA conformation, whereas in the specific complex it is bent by 36°.
 
  The above figures are reprinted by permission from the AAAs: Science (2004, 305, 386-389) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

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PDB codes: 3q01 3q05 3q06
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PDB code: 2ko0
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PDB codes: 2v57 2wgb
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PDB code: 3ebc
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mRNA decapping is promoted by an RNA-binding channel in Dcp2.
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PDB code: 2jvb
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Thermodynamic characterization of specific interactions between the human Lon protease and G-quartet DNA.
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Predicting transcription factor specificity with all-atom models.
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Prediction of TF target sites based on atomistic models of protein-DNA complexes.
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Spatial effects on the speed and reliability of protein-DNA search.
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Eukaryotic membrane tethers revisited using magnetic tweezers.
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A quantitative study of lambda-phage SWITCH and its components.
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Human topoisomerase I C-terminal domain fragment containing the active site tyrosine is a molten globule: implication for the formation of competent productive complex.
  J Struct Biol, 159, 111-121.  
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Energetics of the protein-DNA-water interaction.
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Putting numbers on the network connections.
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The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain.
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PDB code: 2jsp
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DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.
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DNA sequence-specific recognition by a transcriptional regulator requires indirect readout of A-tracts.
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From "simple" DNA-protein interactions to the macromolecular machines of gene expression.
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A single-quantum methyl 13C-relaxation dispersion experiment with improved sensitivity.
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Intrinsic disorder and functional proteomics.
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BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanning.
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PDB code: 2p0j
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Multiple modes of interaction between the methylated DNA binding protein MeCP2 and chromatin.
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Effects of estradiol and 4-hydroxytamoxifen on the conformation, thermal stability, and DNA recognition of estrogen receptor beta.
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PDB codes: 2ivh 2ivk
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Solvated docking: introducing water into the modelling of biomolecular complexes.
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Data-driven docking for the study of biomolecular complexes.
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Protein-DNA recognition patterns and predictions.
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PDB codes: 1u8b 1zgw
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PDB codes: 1q39 1q3b 1q3c
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PDB codes: 1yf3 1yfj 1yfl
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Promoter architecture and response to a positive regulator of archaeal transcription.
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Native-state dynamics of the ubiquitin family: implications for function and evolution.
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Altered specificity in DNA binding by the lac repressor: a mutant lac headpiece that mimics the gal repressor.
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PDB code: 2bjc
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Homeodomain revisited: a lesson from disease-causing mutations.
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Single-molecule studies of repressor-DNA interactions show long-range interactions.
  Proc Natl Acad Sci U S A, 102, 9796-9801.  
15653425 E.J.Helmreich (2004).
Structural flexibility of small GTPases. Can it explain their functional versatility?
  Biol Chem, 385, 1121-1136.  
15465864 M.Slutsky, and L.A.Mirny (2004).
Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.
  Biophys J, 87, 4021-4035.  
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