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PDBsum entry 2cgp

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protein dna_rna ligands links
Transcription/DNA PDB id
2cgp
Jmol
Contents
Protein chain
200 a.a. *
DNA/RNA
Ligands
CMP ×2
Waters ×149
* Residue conservation analysis
PDB id:
2cgp
Name: Transcription/DNA
Title: Catabolite gene activator protein/DNA complex, adenosine-3', 5'-cyclic-monophosphate
Structure: DNA (5'-d( Gp Tp Cp Ap Cp Ap Tp Tp Ap Ap T)-3'). Chain: b. Engineered: yes. DNA (5'- d( Ap Tp Tp Ap Ap Tp Gp Tp Gp Ap Cp Ap Tp Ap T)-3'). Chain: c. Engineered: yes. Protein (catabolite gene activator protein). Chain: a
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.20Å     R-factor:   0.237     R-free:   0.296
Authors: J.M.Passner,T.A.Steitz
Key ref:
J.M.Passner and T.A.Steitz (1997). The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer. Proc Natl Acad Sci U S A, 94, 2843-2847. PubMed id: 9096308 DOI: 10.1073/pnas.94.7.2843
Date:
31-Jan-97     Release date:   04-Feb-98    
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: 10.1073/pnas.94.7.2843 Proc Natl Acad Sci U S A 94:2843-2847 (1997)
PubMed id: 9096308  
 
 
The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer.
J.M.Passner, T.A.Steitz.
 
  ABSTRACT  
 
The 2.2 A resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with cAMP and a 46-bp DNA fragment reveals a second cAMP molecule bound to each protein monomer. The second cAMP is in the syn conformation and is located on the DNA binding domain interacting with the helix-turn-helix, a beta-hairpin from the regulatory domain and the DNA (via water molecules). The presence of this second cAMP site resolves the apparent discrepancy between the NMR and x-ray data on the conformation of cAMP, and explains the cAMP concentration-dependent behaviors of the protein. In addition, this site's close proximity to mutations affecting transcriptional activation and its water-mediated interactions with a DNA recognition residue (E181) and DNA raise the possibility that this site has biological relevance.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. A MOLSCRIPT (4) ribbon drawing of the CAP dimer bound to DNA and the two cAMP molecules (magenta) per monomer, one labeled^ SYN and the other, ANTI. In one monomer, the larger N-terminal domain is yellow, and the smaller C-terminal domain is blue, while^ the DNA half-site bound to it is light gray. The other subunit is green and the DNA bound to it is dark gray. The syn-cAMP lies on the helix-turn-helix and close to the DNA and a loop from the^ N-terminal domain. The DNA sequence of the half-site is 5 -ATGTCACATTAATTGCGTTGCGC-3 .
Figure 2.
Fig. 2. Stereo view of the 2F[o]-F[c] "omit" electron density map at 2.2 Å resolution from which the syn-cAMP (ball-and-stick) was first identified. The density, contoured at 1.2 , was computed using experimentally determined phases from 25 to 8 Å and phases from 8 to 2.2 Å derived from the protein and DNA coordinates alone^ before any coordinates of the syn-cAMP were included in the phase^ and amplitude calculation.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20028978 M.Stapleton, I.Haq, D.M.Hunt, K.B.Arnvig, P.J.Artymiuk, R.S.Buxton, and J.Green (2010).
Mycobacterium tuberculosis cAMP receptor protein (Rv3676) differs from the Escherichia coli paradigm in its cAMP binding and DNA binding properties and transcription activation properties.
  J Biol Chem, 285, 7016-7027.  
20478828 P.Ozbek, S.Soner, B.Erman, and T.Haliloglu (2010).
DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues.
  Nucleic Acids Res, 38, W417-W423.  
20512974 T.J.Sjoberg, A.P.Kornev, and S.S.Taylor (2010).
Dissecting the cAMP-inducible allosteric switch in protein kinase A RIalpha.
  Protein Sci, 19, 1213-1221.
PDB code: 3iia
19594171 A.J.Lee, R.W.Clark, H.Youn, S.Ponter, and J.N.Burstyn (2009).
Guanidine hydrochloride-induced unfolding of the three heme coordination states of the CO-sensing transcription factor, CooA.
  Biochemistry, 48, 6585-6597.  
19805344 H.Sharma, S.Yu, J.Kong, J.Wang, and T.A.Steitz (2009).
Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.
  Proc Natl Acad Sci U S A, 106, 16604-16609.
PDB codes: 3fwe 3hif
19432802 J.D.Radolf, and D.C.Desrosiers (2009).
Treponema pallidum, the stealth pathogen, changes, but how?
  Mol Microbiol, 72, 1081-1086.  
  19309730 J.E.Seedorff, M.E.Rodgers, and R.Schleif (2009).
Opposite allosteric mechanisms in TetR and CAP.
  Protein Sci, 18, 775-781.  
19403523 R.Das, S.Chowdhury, M.T.Mazhab-Jafari, S.Sildas, R.Selvaratnam, and G.Melacini (2009).
Dynamically driven ligand selectivity in cyclic nucleotide binding domains.
  J Biol Chem, 284, 23682-23696.  
19955406 S.Mesa, L.Reutimann, H.M.Fischer, and H.Hennecke (2009).
Posttranslational control of transcription factor FixK2, a key regulator for the Bradyrhizobium japonicum-soybean symbiosis.
  Proc Natl Acad Sci U S A, 106, 21860-21865.  
19671703 T.I.Brelidze, A.E.Carlson, and W.N.Zagotta (2009).
Absence of direct cyclic nucleotide modulation of mEAG1 and hERG1 channels revealed with fluorescence and electrophysiological methods.
  J Biol Chem, 284, 27989-27997.  
18699868 Y.Agari, A.Kashihara, S.Yokoyama, S.Kuramitsu, and A.Shinkai (2008).
Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator.
  Mol Microbiol, 70, 60-75.
PDB code: 2zcw
18514225 Y.Shao, L.S.Feldman-Cohen, and R.Osuna (2008).
Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site.
  J Mol Biol, 380, 327-339.  
17763923 Y.Tutar (2008).
Chemical Linkage at Allosteric Activation of E. coli cAMP Receptor Protein.
  Protein J, 27, 21-29.  
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.  
17531094 A.Del Sol, M.J.Araúzo-Bravo, D.Amoros, and R.Nussinov (2007).
Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages.
  Genome Biol, 8, R92.  
17375187 I.Laponogov, D.A.Veselkov, M.K.Sohi, X.S.Pan, A.Achari, C.Yang, J.D.Ferrara, L.M.Fisher, and M.R.Sanderson (2007).
Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target.
  PLoS ONE, 2, e301.
PDB code: 2nov
17562313 L.Zhou, and S.A.Siegelbaum (2007).
Gating of HCN channels by cyclic nucleotides: residue contacts that underlie ligand binding, selectivity, and efficacy.
  Structure, 15, 655-670.  
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
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.  
16500960 M.Berrera, S.Pantano, and P.Carloni (2006).
cAMP Modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations.
  Biophys J, 90, 3428-3433.  
15618393 H.M.Berman, L.F.Ten Eyck, D.S.Goodsell, N.M.Haste, A.Kornev, and S.S.Taylor (2005).
The cAMP binding domain: an ancient signaling module.
  Proc Natl Acad Sci U S A, 102, 45-50.  
16339893 J.S.Hu, H.Feng, W.Zeng, G.X.Lin, and X.G.Xi (2005).
Solution structure of a multifunctional DNA- and protein-binding motif of human Werner syndrome protein.
  Proc Natl Acad Sci U S A, 102, 18379-18384.
PDB code: 2axl
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.  
15556974 S.B.Dixit, and D.L.Beveridge (2005).
Axis curvature and ligand induced bending in the CAP-DNA oligomers.
  Biophys J, 88, L04-L06.  
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.  
15229894 D.McMullan, R.Schwarzenbacher, L.Jaroszewski, F.von Delft, H.E.Klock, J.Vincent, K.Quijano, P.Abdubek, E.Ambing, T.Biorac, L.S.Brinen, J.M.Canaves, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, S.Eshaghi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, C.Karlak, E.Koesema, A.Kreusch, P.Kuhn, I.Levin, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, R.Reyes, F.Rezezadeh, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, S.A.Lesley, and I.A.Wilson (2004).
Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution.
  Proteins, 56, 615-618.
PDB code: 1o5u
15353565 G.P.Roberts, H.Youn, and R.L.Kerby (2004).
CO-sensing mechanisms.
  Microbiol Mol Biol Rev, 68, 453-473.  
12653996 A.Polit, U.Błaszczyk, and Z.Wasylewski (2003).
Steady-state and time-resolved fluorescence studies of conformational changes induced by cyclic AMP and DNA binding to cyclic AMP receptor protein from Escherichia coli.
  Eur J Biochem, 270, 1413-1423.  
12748944 M.Snapyan, M.Lecocq, L.Guével, M.C.Arnaud, A.Ghochikyan, and V.Sakanyan (2003).
Dissecting DNA-protein and protein-protein interactions involved in bacterial transcriptional regulation by a sensitive protein array method combining a near-infrared fluorescence detection.
  Proteomics, 3, 647-657.  
12022869 A.Dong, J.M.Malecki, L.Lee, J.F.Carpenter, and J.C.Lee (2002).
Ligand-induced conformational and structural dynamics changes in Escherichia coli cyclic AMP receptor protein.
  Biochemistry, 41, 6660-6667.  
11979597 N.Fujimoto, A.Toyama, and H.Takeuchi (2002).
Binding modes of cyclic AMP and environments of tryptophan residues in 1:1 and 1:2 complexes of cyclic AMP receptor protein and cyclic AMP.
  Biopolymers, 67, 186-196.  
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.  
11877432 R.G.Zhang, Y.Kim, T.Skarina, S.Beasley, R.Laskowski, C.Arrowsmith, A.Edwards, A.Joachimiak, and A.Savchenko (2002).
Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.
  J Biol Chem, 277, 19183-19190.
PDB code: 1mkm
11863432 S.H.Lin, L.Kovac, A.J.Chin, C.C.Chin, and J.C.Lee (2002).
Ability of E. coli cyclic AMP receptor protein to differentiate cyclic nucelotides: effects of single site mutations.
  Biochemistry, 41, 2946-2955.  
11297928 A.Hillisch, M.Lorenz, and S.Diekmann (2001).
Recent advances in FRET: distance determination in protein-DNA complexes.
  Curr Opin Struct Biol, 11, 201-207.  
11343786 J.G.Harman (2001).
Allosteric regulation of the cAMP receptor protein.
  Biochim Biophys Acta, 1547, 1.  
10692335 A.N.Naimushin, B.S.Fujimoto, and J.M.Schurr (2000).
Dynamic bending rigidity of a 200-bp DNA in 4 mM ionic strength: a transient polarization grating study.
  Biophys J, 78, 1498-1518.  
11076538 H.S.Won, T.Yamazaki, T.W.Lee, M.K.Yoon, S.H.Park, Y.Kyogoku, and B.J.Lee (2000).
Structural understanding of the allosteric conformational change of cyclic AMP receptor protein by cyclic AMP binding.
  Biochemistry, 39, 13953-13962.  
  10091654 N.Baichoo, and T.Heyduk (1999).
Mapping cyclic nucleotide-induced conformational changes in cyclicAMP receptor protein by a protein footprinting technique using different chemical proteases.
  Protein Sci, 8, 518-528.  
  9440505 X.Zhang, and R.Schleif (1998).
Catabolite gene activator protein mutations affecting activity of the araBAD promoter.
  J Bacteriol, 180, 195-200.  
9591480 J.M.Schurr, J.J.Delrow, B.S.Fujimoto, and A.S.Benight (1997).
The question of long-range allosteric transitions in DNA.
  Biopolymers, 44, 283-308.  
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.