PDBsum entry 2fmy

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protein ligands Protein-protein interface(s) links
DNA binding protein PDB id
Protein chains
218 a.a. *
Waters ×254
* Residue conservation analysis
PDB id:
Name: DNA binding protein
Title: Co-dependent transcription factor cooa from carboxydothermus hydrogenoformans (imidazole-bound form)
Structure: Carbon monoxide oxidation system transcription re cooa-1. Chain: a, b, c, d. Synonym: cooa. Engineered: yes
Source: Carboxydothermus hydrogenoformans. Organism_taxid: 129958. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
2.20Å     R-factor:   0.209     R-free:   0.247
Authors: Y.Higuchi,H.Komori
Key ref:
H.Komori et al. (2007). Crystal structure of CO-sensing transcription activator CooA bound to exogenous ligand imidazole. J Mol Biol, 367, 864-871. PubMed id: 17292914 DOI: 10.1016/j.jmb.2007.01.043
10-Jan-06     Release date:   16-Jan-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q3AB29  (Q3AB29_CARHZ) -  Carbon monoxide oxidation system transcription regulator CooA-1
217 a.a.
218 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   2 terms 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1016/j.jmb.2007.01.043 J Mol Biol 367:864-871 (2007)
PubMed id: 17292914  
Crystal structure of CO-sensing transcription activator CooA bound to exogenous ligand imidazole.
H.Komori, S.Inagaki, S.Yoshioka, S.Aono, Y.Higuchi.
CooA is a CO-dependent transcriptional activator and transmits a CO-sensing signal to a DNA promoter that controls the expression of the genes responsible for CO metabolism. CooA contains a b-type heme as the active site for sensing CO. CO binding to the heme induces a conformational change that switches CooA from an inactive to an active DNA-binding form. Here, we report the crystal structure of an imidazole-bound form of CooA from Carboxydothermus hydrogenoformans (Ch-CooA). In the resting form, Ch-CooA has a six-coordinate ferrous heme with two endogenous axial ligands, the alpha-amino group of the N-terminal amino acid and a histidine residue. The N-terminal amino group of CooA that is coordinated to the heme iron is replaced by CO. This substitution presumably triggers a structural change leading to the active form. The crystal structure of Ch-CooA reveals that imidazole binds to the heme, which replaces the N terminus, as does CO. The dissociated N terminus is positioned approximately 16 A from the heme iron in the imidazole-bound form. In addition, the heme plane is rotated by 30 degrees about the normal of the porphyrin ring compared to that found in the inactive form of Rhodospirillum rubrum CooA. Even though the ligand exchange, imidazole-bound Ch-CooA remains in the inactive form for DNA binding. These results indicate that the release of the N terminus resulting from imidazole binding is not sufficient to activate CooA. The structure provides new insights into the structural changes required to achieve activation.
  Selected figure(s)  
Figure 2.
Figure 2. Stereo view of a ball- and -stick model of the heme and some residues with Im-omitted F[o]–F[c] map. The map is shown in green and contoured at 5σ. The heme exists in a six-coordinate form with His82 and Im ligands. Im is located in the hydrophobic pocket formed by the C-helix and the N-terminal region (from M5 to L7). The N-terminal amino group (N) of Im-bound Ch-CooA is located 16 Å from the heme iron. Carbon, nitrogen, oxygen and sulfur atoms are shown in grey, blue, red and yellow, respectively.
Figure 3.
Figure 3. Comparison of the heme orientation of Ch-CooA (green) and Rr-CooA (cyan). His82 of Ch-CooA and His77 of Rr-CooA are superimposed. The meso α–γ axis is shown as a dotted line. The heme is rotated by vert, similar 30° about the normal of the heme plane in Im-bound Ch-CooA relative to Rr-CooA. In Im-bound Ch-CooA, the heme propionates interact with Lys194 in the DNA-binding domain and Arg84 in the effector-binding domain, while the heme propionate of Rr-CooA interacts with Arg4 in the N-terminal region.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 367, 864-871) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20823675 T.Yamashita (2010).
[Recent studies on gas sensors, CooA, FixL, and Dos].
  Yakugaku Zasshi, 130, 1181-1187.  
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
19239487 S.M.Techtmann, A.S.Colman, and F.T.Robb (2009).
'That which does not kill us only makes us stronger': the role of carbon monoxide in thermophilic microbial consortia.
  Environ Microbiol, 11, 1027-1037.  
19732344 Y.Qin, C.Keenan, and S.K.Farrand (2009).
N- and C-terminal regions of the quorum-sensing activator TraR cooperate in interactions with the alpha and sigma-70 components of RNA polymerase.
  Mol Microbiol, 74, 330-346.  
18688409 S.Aono (2008).
Metal-containing sensor proteins sensing diatomic gas molecules.
  Dalton Trans, (), 3137-3146.  
17720248 M.Ibrahim, M.Kuchinskas, H.Youn, R.L.Kerby, G.P.Roberts, T.L.Poulos, and T.G.Spiro (2007).
Mechanism of the CO-sensing heme protein CooA: new insights from the truncated heme domain and UVRR spectroscopy.
  J Inorg Biochem, 101, 1776-1785.  
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