PDBsum entry 2hkx

Transcription regulator

PDB id: 2hkx

Contents

Protein chains

218 a.a. *

148 a.a. *

Ligands

HEM-CMO

Waters ×58

* Residue conservation analysis

PDB id:

2hkx

Name:

Transcription regulator

Title:

Structure of cooa mutant (n127l/s128l) from carboxydothermus hydrogenoformans

Structure:

Carbon monoxide oxidation system transcription regulator cooa-1. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Carboxydothermus hydrogenoformans. Organism_taxid: 129958. Gene: cooa-1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.30Å R-factor: 0.230 R-free: 0.286

Authors:

N.D.Lanz,M.Borjigin,H.Li,R.L.Kerby,T.L.Poulos,G.P.Roberts

Key ref:

M.Borjigin et al. (2007). Structure-based hypothesis on the activation of the CO-sensing transcription factor CooA. Acta Crystallogr D Biol Crystallogr, 63, 282-287. PubMed id: 17327664 DOI: 10.1107/S0907444906051638

Date:

05-Jul-06 Release date: 06-Mar-07

Protein chain

Q3AB29  (Q3AB29_CARHZ) -  Carbon monoxide oxidation system transcription regulator CooA-1 from Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)

Seq: 217 a.a.

Struc: 218 a.a.*

Protein chain

Q3AB29  (Q3AB29_CARHZ) -  Carbon monoxide oxidation system transcription regulator CooA-1 from Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)

Seq: 217 a.a.

Struc: 148 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.?

DOI no: 10.1107/S0907444906051638

Acta Crystallogr D Biol Crystallogr 63:282-287 (2007)

PubMed id: 17327664

Structure-based hypothesis on the activation of the CO-sensing transcription factor CooA.

M.Borjigin, H.Li, N.D.Lanz, R.L.Kerby, G.P.Roberts, T.L.Poulos.

ABSTRACT

The CooA family of proteins are prokaryotic CO-sensing transcription factors that regulate the expression of genes involved in the utilization of CO as an energy source. They are homodimeric proteins that contain two hemes. Each monomer contains an N-terminal heme-binding domain and a C-terminal DNA-binding domain. Binding of CO to the heme leads to activation by a large reorientation of the DNA-binding domain such that the DNA-binding domain is in position for specific DNA recognition. The crystal structure of CooA from Rhodospirillum rubrum [RrCooA; Lanzilotta et al. (2000), Nature Struct. Biol. 7, 876-880] in the inactive CO-free off-state shows that the N-terminal Pro residue of monomer A coordinates the heme of monomer B and vice versa. It now appears that the CO replaces the Pro ligand and that this change is coupled to the activation process. However, precisely how the replacement of the Pro ligand by CO results in structural changes some 25 A from the CO-binding site remains unknown. Here, the structure of a CooA variant from the thermophilic bacterium Carboxydothermus hydrogenoformans (ChCooA) is reported in which one monomer is fully in the on-state. The N-terminal region that is displaced by CO binding is now positioned between the heme-binding and DNA-binding domains, which requires movement of the N-terminus by approximately 20 A and thus serves as a bridge between the two domains that helps to orient the DNA-binding domain in position for DNA binding.

Selected figure(s)

Figure 1.
Figure 1 Crystal structure of RrCooA. (a) In monomer A (dark) the DNA-binding domain is in the fully extended orientation, while in monomer B (light) the DNA-binding domain is in a bent orientation. The van der Waals spheres are the heme groups. Note the long C helices that form the dimer interface. (b) A close-up view of the C-helical interface, showing the interaction between symmetry-related Leu and Ile residues.

Figure 4.
Figure 4 2F[o] - F[c] electron-density map contoured at 1 and F[o] - F[c] map contoured at 3.0 (red) around the heme site. (a) The electron densities for both Cys80 and His82 are continuous with the iron, although the geometry and the distance between Cys80 and the iron indicates very weak ligation. Also shown is Asn47 which in inactive RrCooA hydrogen bonds to the His ligand. However, in LL-ChCooA Asn47 is about 4.6 Å from His82. Both 2F[o] - F[c] and F[o] - F[c] density indicate the presence of CO bound to the heme iron. (b) Structure around the CO-binding pocket. Residues shown in yellow are from molecule B, while those in green are from molecule A. The cluster of Leu residues forms a tight hydrophobic pocket around CO that favors a linear Fe-CO bond. Gly122 also contributes to the CO-binding pocket, but is not shown for clarity.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 282-287) copyright 2007.

Figures were selected by an automated process.