PDBsum entry 2h6b

DNA binding protein

PDB id: 2h6b

Contents

Protein chains

239 a.a. *

Ligands

SO4 ×2

3C4 ×2

Waters ×228

* Residue conservation analysis

PDB id:

2h6b

Name:

DNA binding protein

Title:

Crystal structure of oxidized cprk in complex with o- chlorophenolacetic acid

Structure:

Chlorophenol reduction gene k. Chain: a, b. Synonym: cprk. Engineered: yes

Source:

Desulfitobacterium hafniense. Organism_taxid: 49338. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.20Å R-factor: 0.186 R-free: 0.229

Authors:

M.G.Joyce,C.Levy,D.Leys

Key ref:

M.G.Joyce et al. (2006). CprK crystal structures reveal mechanism for transcriptional control of halorespiration. J Biol Chem, 281, 28318-28325. PubMed id: 16803881 DOI: 10.1074/jbc.M602654200

Date:

31-May-06 Release date: 04-Jul-06

Protein chains

Q8RPJ2  (Q8RPJ2_DESHA) -  Putative transcription regulatory protein from Desulfitobacterium hafniense

Seq: 202 a.a.

Struc: 239 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1074/jbc.M602654200

J Biol Chem 281:28318-28325 (2006)

PubMed id: 16803881

CprK crystal structures reveal mechanism for transcriptional control of halorespiration.

M.G.Joyce, C.Levy, K.Gábor, S.M.Pop, B.D.Biehl, T.I.Doukov, J.M.Ryter, H.Mazon, H.Smidt, R.H.van den Heuvel, S.W.Ragsdale, J.van der Oost, D.Leys.

ABSTRACT

Halorespiration is a bacterial respiratory process in which haloorganic compounds act as terminal electron acceptors. This process is controlled at transcriptional level by CprK, a member of the ubiquitous CRP-FNR family. Here we present the crystal structures of oxidized CprK in presence of the ligand ortho-chlorophenolacetic acid and of reduced CprK in absence of this ligand. These structures reveal that highly specific binding of chlorinated, rather than the corresponding non-chlorinated, phenolic compounds in the NH(2)-terminal beta-barrels causes reorientation of these domains with respect to the central alpha-helix at the dimer interface. Unexpectedly, the COOH-terminal DNA-binding domains dimerize in the non-DNA binding state. We postulate the ligand-induced conformational change allows formation of interdomain contacts that disrupt the DNA domain dimer interface and leads to repositioning of the helix-turn-helix motifs. These structures provide a structural framework for further studies on transcriptional control by CRP-FNR homologs in general and of halorespiration regulation by CprK in particular.

Selected figure(s)

Figure 4.
FIGURE 4. Overlay of the NH[2]-terminal domains of both CprK structures. An overlay is shown that was created by superimposition of the B and C -helices of both ligand-free CprK and the CHPA-bound CprK structures with central helices colored blue for both structures, while the NH[2]-terminal -barrel (residues 20-108 for both structures) is colored green for the CHPA-CprK complex and orange for the ligand free CprK. Bound CHPA molecules in the CHPA-CprK structure are represented in atom-colored spheres. To illustrate the motion of the NH[2]-terminal -barrel with respect to the putative position of the HTH motifs in the DNA binding state (by analogy to CRP), the putative HTH motifs are represented in gray.

Figure 7.
FIGURE 7. Binding of ortho-chlorophenolic compounds causes structural rearrangement. A, overlay of a single CHPA-binding site of the ligand-free CprK (color coding same as described for Fig. 1) with a hybrid CprK structure (in gray; see "Results and Discussion"). This clearly illustrates the induced fit in both the NH[2]-terminal -barrel and the C helix residues upon binding of CHPA. B, similar view to A, but only the hybrid structure is displayed, colored-coded as described for Fig. 1. The hydrophobic pocket created by the C helix residues is depicted as a transparent surface. H-bonds between CHPA and CprK are depicted in dashed lines. No direct interaction can be made between CHPA and Lys-133, while the CHPA chloride atom is not ideally placed in the binding pocket. C, similar view to B but for the CHPA-CprK crystal structure. The reorientation of the -barrel has allowed for an additional interaction between CHPA and Lys-133 while positioning the CHPA chloride atom in the center of the hydrophobic cavity.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 28318-28325) copyright 2006.

Figures were selected by the author.