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PDBsum entry 3fwe

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protein ligands Protein-protein interface(s) links
Transcription regulator PDB id
3fwe
Jmol
Contents
Protein chains
202 a.a. *
Ligands
PRO ×2
Waters ×238
* Residue conservation analysis
PDB id:
3fwe
Name: Transcription regulator
Title: Crystal structure of the apo d138l cap mutant
Structure: Catabolite gene activator. Chain: a, b. Synonym: camp receptor protein, camp regulatory protein. Engineered: yes. Mutation: yes
Source: Escherichia coli k-12. Organism_taxid: 83333. Strain: dh5a. Gene: b3357, cap, crp, csm, jw5702. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.230     R-free:   0.277
Authors: H.Sharma,J.Wang,J.Kong,S.Yu,T.Steitz
Key ref:
H.Sharma et al. (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. PubMed id: 19805344 DOI: 10.1073/pnas.0908380106
Date:
17-Jan-09     Release date:   08-Sep-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0ACJ8  (CRP_ECOLI) -  cAMP-activated global transcriptional regulator CRP
Seq:
Struc:
210 a.a.
202 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: 10.1073/pnas.0908380106 Proc Natl Acad Sci U S A 106:16604-16609 (2009)
PubMed id: 19805344  
 
 
Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.
H.Sharma, S.Yu, J.Kong, J.Wang, T.A.Steitz.
 
  ABSTRACT  
 
The binding of cAMP to the Escherichia coli catabolite gene activator protein (CAP) produces a conformational change that enables it to bind specific DNA sequences and regulate transcription, which it cannot do in the absence of the nucleotide. The crystal structures of the unliganded CAP containing a D138L mutation and the unliganded WT CAP were determined at 2.3 and 3.6 A resolution, respectively, and reveal that the two DNA binding domains have dimerized into one rigid body and their two DNA recognition helices become buried. The WT structure shows multiple orientations of this rigid body relative to the nucleotide binding domain supporting earlier biochemical data suggesting that the inactive form exists in an equilibrium among different conformations. Comparison of the structures of the liganded and unliganded CAP suggests that cAMP stabilizes the active DNA binding conformation of CAP through the interactions that the N(6) of the adenosine makes with the C-helices. These interactions are associated with the reorientation and elongation of the C-helices that precludes the formation of the inactive structure.
 
  Selected figure(s)  
 
Figure 2.
Comparison of the inactive (Left) and the active forms of CAP (Right). (A) Schematic representation of CAP shows [beta]-strands as arrows and [alpha]-helices as coils. The cAMP is shown in ball and stick representation. DNA is shown as transparent spheres and its bases are colored slate blue. (B) The cAMP binding domains and DNA have been excluded to emphasize the orientations of the DNA binding domains and the C-helices. Residues capping the C- and D-helices and cAMP are shown as ball and stick. In the inactive form, K130 is located at the C termini of the C-helices, whereas in the active form, D138 is located at the N termini of the D-helices. (C) The C terminus of the C-helix, the N terminus of the D-helix, and the hinge residues of one protomer of the inactive and the active form.
Figure 4.
The cAMP induced conformational changes of CAP. The side view of CAP is shown. Structure of the unliganded CAP (Left) and of the liganded CAP (Right). A superposition of these two structures along their C-helices is shown in the middle of the figure. The unliganded structure is solid, whereas the liganded structure is transparent. To emphasize the conformational changes on cAMP binding, only the C-, D-, and F-helices are shown.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22773105 H.J.Lee, P.T.Lang, S.M.Fortune, C.M.Sassetti, and T.Alber (2012).
Cyclic AMP regulation of protein lysine acetylation in Mycobacterium tuberculosis.
  Nat Struct Mol Biol, 19, 811-818.
PDB codes: 4ava 4avb 4avc
21265778 I.T.Cadby, S.J.Busby, and J.A.Cole (2011).
An HcpR homologue from Desulfovibrio desulfuricans and its possible role in nitrate reduction and nitrosative stress.
  Biochem Soc Trans, 39, 224-229.  
20716687 J.L.Llácer, J.Espinosa, M.A.Castells, A.Contreras, K.Forchhammer, and V.Rubio (2010).
Structural basis for the regulation of NtcA-dependent transcription by proteins PipX and PII.
  Proc Natl Acad Sci U S A, 107, 15397-15402.
PDB codes: 2xg8 2xgx 2xhk 2xko 2xkp
20616047 M.X.Zhao, Y.L.Jiang, Y.X.He, Y.F.Chen, Y.B.Teng, Y.Chen, C.C.Zhang, and C.Z.Zhou (2010).
Structural basis for the allosteric control of the global transcription factor NtcA by the nitrogen starvation signal 2-oxoglutarate.
  Proc Natl Acad Sci U S A, 107, 12487-12492.
PDB codes: 3la2 3la3 3la7
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.