PDBsum entry 1o3s

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protein dna_rna ligands links
Gene regulation/DNA PDB id
Protein chain
200 a.a. *
CMP ×2
Waters ×36
* Residue conservation analysis
PDB id:
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)
3.00Å     R-factor:   0.260     R-free:   0.308
Authors: S.Chen,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: alteration of DNA binding specificity through alteration of DNA kinking. J Mol Biol, 314, 75-82. PubMed id: 11724533 DOI: 10.1006/jmbi.2001.5090
18-Mar-03     Release date:   08-Apr-03    
Supersedes: 1db9
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0ACJ8  (CRP_ECOLI) -  cAMP-activated global transcriptional regulator CRP
210 a.a.
200 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!
  Cellular component     intracellular   1 term 
  Biological process     transcription, DNA-dependent   5 terms 
  Biochemical function     nucleotide binding     5 terms  


DOI no: 10.1006/jmbi.2001.5090 J Mol Biol 314:75-82 (2001)
PubMed id: 11724533  
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking.
S.Chen, A.Gunasekera, X.Zhang, T.A.Kunkel, R.H.Ebright, H.M.Berman.
The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a 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, 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' ("primary kink"). CAP recognizes the base-pair immediately 5' to the primary-kink site, T:A(6), through an "indirect-readout" mechanism involving sequence effects on the energetics of primary-kink formation. CAP recognizes the base-pair immediately 3' to the primary-kink site, G:C(7), through a "direct-readout" mechanism involving formation of a hydrogen bond between Glu181 of CAP and G:C(7). Here, we report that substitution of the carboxylate side-chain of Glu181 of CAP by the one-methylene-group-shorter carboxylate side-chain of Asp changes DNA binding specificity at position 6 of the DNA half site, changing specificity for T:A(6) to specificity for C:G(6), and we report a crystallographic analysis defining the structural basis of the change in specificity. The Glu181-->Asp substitution eliminates the primary kink and thus eliminates indirect-readout-based specificity for T:A(6). The Glu181-->Asp substitution does not eliminate hydrogen-bond formation with G:C(7), and thus does not eliminate direct-readout-based specificity for G:C(7).
  Selected figure(s)  
Figure 1.
Figure 1. Least-squares superimposition of structures of the CAP-DNA (blue), CAP-[6C;17G]DNA (green) and [Asp181]CAP-[6C;17G]DNA (red) complexes in space group P3[1]21. CAP is shown in a ribbon representation, cAMP bound to CAP (two molecules per CAP subunit; see Chen et al[11]. and Passner & Steitz [16]) is shown in black. The Figure was generated using MOLSCRIPT [24].
Figure 3.
Figure 3. DNA-helical parameters for the CAP-DNA, CAP-[6C;17G]DNA, and [Asp181]CAP-[6C;17G]DNA complexes. (a) Roll; (b) twist; (c) roll versus twist. DNA sequences and colors are as in Figure 1.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 314, 75-82) 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.  
20338852 P.Kumar, D.C.Joshi, M.Akif, Y.Akhter, S.E.Hasnain, and S.C.Mande (2010).
Mapping conformational transitions in cyclic AMP receptor protein: crystal structure and normal-mode analysis of Mycobacterium tuberculosis apo-cAMP receptor protein.
  Biophys J, 98, 305-314.
PDB code: 3h3u
19734309 N.Hugouvieux-Cotte-Pattat, and S.Charaoui-Boukerzaza (2009).
Catabolism of raffinose, sucrose, and melibiose in Erwinia chrysanthemi 3937.
  J Bacteriol, 191, 6960-6967.  
18762194 A.C.Babic, E.J.Little, V.M.Manohar, J.Bitinaite, and N.C.Horton (2008).
DNA distortion and specificity in a sequence-specific endonuclease.
  J Mol Biol, 383, 186-204.
PDB codes: 3e3y 3e40 3e41 3e42 3e43 3e44 3e45
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.  
17277419 K.A.Aeling, N.R.Steffen, M.Johnson, G.W.Hatfield, R.H.Lathrop, and D.F.Senear (2007).
DNA deformation energy as an indirect recognition mechanism in protein-DNA interactions.
  IEEE/ACM Trans Comput Biol Bioinform, 4, 117-125.  
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.  
17766249 S.Fujii, H.Kono, S.Takenaka, N.Go, and A.Sarai (2007).
Sequence-dependent DNA deformability studied using molecular dynamics simulations.
  Nucleic Acids Res, 35, 6063-6074.  
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.  
16675462 H.K.Joshi, C.Etzkorn, L.Chatwell, J.Bitinaite, and N.C.Horton (2006).
Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.
  J Biol Chem, 281, 23852-23869.
PDB codes: 2gie 2gig 2gih 2gii 2gij
16528102 W.A.Weihofen, A.Cicek, F.Pratto, J.C.Alonso, and W.Saenger (2006).
Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription.
  Nucleic Acids Res, 34, 1450-1458.
PDB codes: 2bnw 2bnz 2cax
15869395 A.Sarai, and H.Kono (2005).
Protein-DNA recognition patterns and predictions.
  Annu Rev Biophys Biomol Struct, 34, 379-398.  
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.  
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.  
14673097 S.Y.Reddy, S.Obika, and T.C.Bruice (2003).
Conformations and dynamics of Ets-1 ETS domain-DNA complexes.
  Proc Natl Acad Sci U S A, 100, 15475-15480.  
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 code is shown on the right.