PDBsum entry 1v9y

Signaling protein

PDB id: 1v9y

Contents

Protein chains

103 a.a. *

Ligands

HEM ×2

Waters ×349

* Residue conservation analysis

PDB id:

1v9y

Name:

Signaling protein

Title:

Crystal structure of the heme pas sensor domain of ec dos (ferric form)

Structure:

Heme pas sensor protein. Chain: a, b. Fragment: heme pas domain. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: dos. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.32Å R-factor: 0.163 R-free: 0.219

Authors:

H.Kurokawa,D.S.Lee,M.Watanabe,I.Sagami,B.Mikami,C.S.Raman,T.Shimizu

Key ref:

H.Kurokawa et al. (2004). A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor. J Biol Chem, 279, 20186-20193. PubMed id: 14982921 DOI: 10.1074/jbc.M314199200

Date:

04-Feb-04 Release date: 25-May-04

Protein chains

P76129  (DOSP_ECOLI) -  Oxygen sensor protein DosP from Escherichia coli (strain K12)

Seq: 799 a.a.

Struc: 103 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.4.52 - cyclic-guanylate-specific phosphodiesterase.
• Reaction: 3',3'-c-di-GMP + H2O = 5'-phosphoguanylyl(3'->5')guanosine + H⁺
• Cofactor: Heme; Mg(2+); Mn(2+)

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity) Mg(2+) Mn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M314199200

J Biol Chem 279:20186-20193 (2004)

PubMed id: 14982921

A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor.

H.Kurokawa, D.S.Lee, M.Watanabe, I.Sagami, B.Mikami, C.S.Raman, T.Shimizu.

ABSTRACT

PAS domains, which have been identified in over 1100 proteins from all three kingdoms of life, convert various input stimuli into signals that propagate to downstream components by modifying protein-protein interactions. One such protein is the Escherichia coli redox sensor, Ec DOS, a phosphodiesterase that degrades cyclic adenosine monophosphate in a redox-dependent manner. Here we report the crystal structures of the heme PAS domain of Ec DOS in both inactive Fe(3+) and active Fe(2+) forms at 1.32 and 1.9 A resolution, respectively. The protein folds into a characteristic PAS domain structure and forms a homodimer. In the Fe(3+) form, the heme iron is ligated to a His-77 side chain and a water molecule. Heme iron reduction is accompanied by heme-ligand switching from the water molecule to a side chain of Met-95 from the FG loop. Concomitantly, the flexible FG loop is significantly rigidified, along with a change in the hydrogen bonding pattern and rotation of subunits relative to each other. The present data led us to propose a novel redox-regulated molecular switch in which local heme-ligand switching may trigger a global "scissor-type" subunit movement that facilitates catalytic control.

Selected figure(s)

Figure 2.
FIG. 2. Dimer of Ec DOSH and redox-induced changes at the heme distal site. a, left, Fe^3+ form of the Ec DOSH dimer. The 2-fold axis of subunits is specified as a blue stick. Right, the view after 90° rotation of the left figure. Heme and proximal histidine 77 are shown as a ball-and-stick model. Disordered FG loop regions are indicated by blue broken lines. Water molecules are represented by spheres (cyan). N, N terminus; C, C terminus. b, close-up view of the heme site of the Fe^3+ form of Ec DOSH (left); the same region of the Fe^2+ form (right). FG loop regions are rigidified in the Fe^2+ form (cyan). The distal axial ligand is replaced by Met-95, as indicated in the sphere model.

Figure 4.
FIG. 4. Reorganization of the hydrogen bond network at the heme distal site near the dimer interface. a, comparison of heme distal sites between Fe^3+ (cyan) and Fe^2+ (yellow) forms of Ec DOSH. Residues 31-85 and 97-132 of subunit I in each form were superimposed. Residues in subunit II are colored in blue for the Fe^3+ form and orange for the Fe^2+ form. Hydrogen bonds are presented as dotted lines. Met-95 coordination to the heme iron upon reduction induces reorganization of the hydrogen bond network at the heme distal site. Side chains of Phe-113 and Leu-115 move slightly to adjust to heme-ligand switching. These changes induce hydrogen bond formation between Phe-113 and Arg-131. No effects were observed on the hydrogen bond between Ser-116 and Met-30. The buried dimer surface areas of the Fe^3+ form (b) and Fe^2+ form (c) of subunit I are shown. Distances between the surfaces of each subunit were calculated with MOLMOL and ranged from <2 Å (red) to >7 Å (blue). Met-30 and Arg-131 of subunit II are presented as a stick model.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 20186-20193) copyright 2004.

Figures were selected by the author.