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PDBsum entry 1o3r

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protein dna_rna ligands links
Gene regulation/DNA PDB id
1o3r
Jmol
Contents
Protein chain
200 a.a. *
DNA/RNA
Ligands
CMP ×2
Waters ×54
* Residue conservation analysis
PDB id:
1o3r
Name: Gene regulation/DNA
Title: Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes
Structure: 5'-d( Ap Ap Ap Ap Ap Tp Gp Cp Gp Ap T)-3'. Chain: b. Engineered: yes. 5'- d( Cp Tp Ap Gp Ap Tp Cp Gp Cp Ap Tp Tp Tp Tp T)-3'. Chain: c. Engineered: yes. Catabolite gene activator protein. Chain: a.
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
3.00Å     R-factor:   0.233     R-free:   0.283
Authors: S.Chen,J.Vojtechovsky,G.N.Parkinson,R.H.Ebright,H.M.Berman
Key ref:
S.Chen et al. (2001). Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking. J Mol Biol, 314, 63-74. PubMed id: 11724532 DOI: 10.1006/jmbi.2001.5089
Date:
18-Mar-03     Release date:   08-Apr-03    
Supersedes: 1db8
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0ACJ8  (CRP_ECOLI) -  cAMP-activated global transcriptional regulator CRP
Seq:
Struc:
210 a.a.
200 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   5 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
DOI no: 10.1006/jmbi.2001.5089 J Mol Biol 314:63-74 (2001)
PubMed id: 11724532  
 
 
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking.
S.Chen, J.Vojtechovsky, G.N.Parkinson, R.H.Ebright, H.M.Berman.
 
  ABSTRACT  
 
The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 of the DNA half-site 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results in formation of a sharp DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site. The consensus base-pair T:A at position 6 and the consensus base-pair G:C at position 7 form a T:A/G:C step, which is known to be associated with DNA flexibility. It has been proposed that specificity for T:A at position 6 is a consequence of formation of the DNA kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step on the geometry of DNA kinking, or the energetics of DNA kinking. In this work, we determine crystallographic structures of CAP-DNA complexes having the consensus base-pair T:A at position 6 or the non-consensus base-pair C:G at position 6. We show that complexes containing T:A or C:G at position 6 exhibit similar overall DNA bend angles and local geometries of DNA kinking. We infer that indirect readout in this system does not involve differences in the geometry of DNA kinking but, rather, solely differences in the energetics of DNA kinking. We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. CAP-DNA complexes having and not having the T:A/G:C base-pair step at the primary-kink site. (a) DNA fragments used for crystallization in space group C222[1]. (b) Least-squares superimposition of structures of CAP-DNA (cyan) and CAP-[6C;17G]DNA (yellow; position 6 of each DNA half-site in red) complexes in space group C222[1]. (c) DNA fragments used for crystallization in space group P3[1]21. (d) Least-squares superimposition of structures of CAP-DNA (blue) and CAP-[6C;17G]DNA (green; position 6 of each DNA half-site in red) complexes in space group P3[1]21. In (a) and (c) the positions of the nicks in the DNA are shown as vertical bars. The o indicates the position of the 2-fold symmetry axis in the sequence. In (b) and (d), CAP is shown in a ribbon representation, and bound cAMP. One molecule per CAP subunit in space group C222[1][13, 14 and 15]; two molecules per CAP subunit in space group P3[1]21. The same positions and the same number of molecules of cAMP were seen in another CAP-DNA complex in a trigonal space group[28]. (b) and (d) were generated using MOLSCRIPT [45].
Figure 3.
Figure 3. Details of CAP-DNA interactions in complexes having and not having the T:A/G:C base-pair step at the primary-kink site. Panels illustrate the second a-helix of the helix-turn-helix motif of CAP (recognition helix) and positions 4 to 8 of the DNA half-site. For reference, the primary-kink is located between position 6 and 7 of the DNA half-site. (a) CAP-DNA (top), CAP-[6C;17G]DNA (middle) and superimposed CAP-DNA and CAP-[6C;17G]DNA (bottom; colors as in Figure 1) complexes in space group C222[1] (half-complex A). (b) CAP-DNA (top), CAP-[6C;17G]DNA (middle) and superimposed CAP-DNA and CAP-[6C;17G]DNA (bottom; colors as in Figure 1) complexes in space group C222[1] (half-complex B). (c) CAP-DNA (top), CAP-[6C;17G]DNA (middle) and superimposed CAP-DNA and CAP-[6C;17G]DNA (bottom; colors as in Figure 1) complexes in space group P3[1]21. Stereodiagrams were generated using MOLSCRIPT[45]. The cutoff distance used for defining hydrogen bonds (violet broken lines) was 3.5 Å.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 63-74) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21208404 A.Marathe, and M.Bansal (2011).
An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression.
  BMC Struct Biol, 11, 1.  
21247872 J.S.Mitchell, C.A.Laughton, and S.A.Harris (2011).
Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA.
  Nucleic Acids Res, 39, 3928-3938.  
18653536 S.Lindemose, P.E.Nielsen, and N.E.Møllegaard (2008).
Dissecting direct and indirect readout of cAMP receptor protein DNA binding using an inosine and 2,6-diaminopurine in vitro selection system.
  Nucleic Acids Res, 36, 4797-4807.  
18931124 T.Koyanagi, T.Katayama, H.Suzuki, and H.Kumagai (2008).
Altered oligomerization properties of N316 mutants of Escherichia coli TyrR.
  J Bacteriol, 190, 8238-8243.  
18600227 X.J.Lu, and W.K.Olson (2008).
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.
  Nat Protoc, 3, 1213-1227.  
18338329 Y.Tutar (2008).
Syn, anti, and finally both conformations of cyclic AMP are involved in the CRP-dependent transcription initiation mechanism in E. coli lac operon.
  Cell Biochem Funct, 26, 399-405.  
17462013 F.Cava, O.Laptenko, S.Borukhov, Z.Chahlafi, E.Blas-Galindo, P.Gómez-Puertas, and J.Berenguer (2007).
Control of the respiratory metabolism of Thermus thermophilus by the nitrate respiration conjugative element NCE.
  Mol Microbiol, 64, 630-646.  
17074757 R.Das, and G.Melacini (2007).
A model for agonism and antagonism in an ancient and ubiquitous cAMP-binding domain.
  J Biol Chem, 282, 581-593.  
17182741 R.Das, V.Esposito, M.Abu-Abed, G.S.Anand, S.S.Taylor, and G.Melacini (2007).
cAMP activation of PKA defines an ancient signaling mechanism.
  Proc Natl Acad Sci U S A, 104, 93-98.  
16427082 A.A.Napoli, C.L.Lawson, R.H.Ebright, and H.M.Berman (2006).
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.
  J Mol Biol, 357, 173-183.
PDB codes: 1zrc 1zrd 1zre 1zrf
17068078 A.D.Cameron, and R.J.Redfield (2006).
Non-canonical CRP sites control competence regulons in Escherichia coli and many other gamma-proteobacteria.
  Nucleic Acids Res, 34, 6001-6014.  
16586530 K.Fukuzawa, Y.Komeiji, Y.Mochizuki, A.Kato, T.Nakano, and S.Tanaka (2006).
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: ab initio fragment molecular orbital study.
  J Comput Chem, 27, 948-960.  
15720385 M.Tworzydło, A.Polit, J.Mikołajczak, and Z.Wasylewski (2005).
Fluorescence quenching and kinetic studies of conformational changes induced by DNA and cAMP binding to cAMP receptor protein from Escherichia coli.
  FEBS J, 272, 1103-1116.  
15731390 S.B.Dixit, D.Q.Andrews, and D.L.Beveridge (2005).
Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences.
  Biophys J, 88, 3147-3157.  
15202939 A.Höglund, and O.Kohlbacher (2004).
From sequence to structure and back again: approaches for predicting protein-DNA binding.
  Proteome Sci, 2, 3.  
15102444 C.L.Lawson, D.Swigon, K.S.Murakami, S.A.Darst, H.M.Berman, and R.H.Ebright (2004).
Catabolite activator protein: DNA binding and transcription activation.
  Curr Opin Struct Biol, 14, 10-20.  
12060684 F.A.Gollmick, M.Lorenz, U.Dornberger, J.von Langen, S.Diekmann, and H.Fritzsche (2002).
Solution structure of dAATAA and dAAUAA DNA bulges.
  Nucleic Acids Res, 30, 2669-2677.
PDB codes: 1jrv 1jrw 1js5 1js7
12072566 K.M.Thayer, and D.L.Beveridge (2002).
Hidden Markov models from molecular dynamics simulations on DNA.
  Proc Natl Acad Sci U S A, 99, 8642-8647.  
11972323 P.R.Hardwidge, J.M.Zimmerman, and L.J.Maher (2002).
Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein.
  Nucleic Acids Res, 30, 1879-1885.  
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.