PDBsum entry 2w3d

Transferase

PDB id: 2w3d

Contents

Protein chains

148 a.a. *

Ligands

HEM ×2

Metals

_CA

Waters ×118

* Residue conservation analysis

PDB id:

2w3d

Name:

Transferase

Title:

Structure of the first gaf domain of mycobacterium tuberculosis doss

Structure:

Two component sensor histidine kinase devs (gaf family protein). Chain: a, b. Fragment: gaf domain, residues 63-210. Synonym: doss. Engineered: yes. Other_details: d63 to k120 of doss with additional gamdp sequence at the n-terminus due to cloning procedure

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.216 R-free: 0.279

Authors:

B.S.Kang,H.Y.Cho,H.J.Cho

Key ref:

H.Y.Cho et al. (2009). Structural Insight into the Heme-based Redox Sensing by DosS from Mycobacterium tuberculosis. J Biol Chem, 284, 13057-13067. PubMed id: 19276084 DOI: 10.1074/jbc.M808905200

Date:

12-Nov-08 Release date: 10-Mar-09

Protein chains

P9WGK3  (DEVS_MYCTU) -  Oxygen sensor histidine kinase response regulator DevS/DosS from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 578 a.a.

Struc: 148 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.13.3 - histidine kinase.
• Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine

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

reference

DOI no: 10.1074/jbc.M808905200

J Biol Chem 284:13057-13067 (2009)

PubMed id: 19276084

Structural Insight into the Heme-based Redox Sensing by DosS from Mycobacterium tuberculosis.

H.Y.Cho, H.J.Cho, Y.M.Kim, J.I.Oh, B.S.Kang.

ABSTRACT

Mycobacterium tuberculosis is thought to undergo transformation into its non-replicating persistence state under the influence of hypoxia or nitric oxide (NO). This transformation is thought to be mediated via two sensor histidine kinases, DosS and DosT, each of which contains two GAF domains that are responsible for detecting oxygen tension. In this study we determined the crystal structures of the first GAF domain (GAF-A) of DosS, which shows an interaction with a heme. A b-type heme was embedded in a hydrophobic cavity of the GAF-A domain and was roughly perpendicular to the beta-sheet of the GAF domain. The heme iron was liganded by His-149 at the proximal heme axial position. The iron, in the oxidized form, was six-coordinated with a water molecule at the distal position. Upon reduction, the iron, in ferrous form, was five-coordinated, and when the GAF domain was exposed to atmospheric O(2), the ferrous form was oxidized to generate the Met form rather than a ferrous O(2)-bound form. Because the heme is isolated inside the GAF domain, its accessibility is restricted. However, a defined hydrogen bond network found at the heme site could accelerate the electron transferability and would explain why DosS was unable to bind O(2). Flavin nucleotides were shown to reduce the heme iron of DosS while NADH was unable to do so. These results suggest that DosS is a redox sensor and detects hypoxic conditions by its reduction.

Selected figure(s)

Figure 2.
Electron density maps around the heme at DosS GAF-A. A, water molecule interacts with the heme iron at the distal position in the native structure. B, ferrous iron is five coordinated in the reduced form of GAF-A. C, upon air exposure, a water molecule ligands the heme iron at the distal position. D, cyanide interacts with the heme at the distal position, and Tyr-171 guides the cyanide interaction. The 2F[o]-F[c] electron density maps were contoured at the 1.5 σ level.

Figure 3.
Interactions of ligand and residues at the heme sites. The numbers next to the dashed lines indicate the distances (Å) between two atoms. The residues are water molecules at the heme sites of the native (A), selenomethionine-substituted (B), reduced by sodium dithionite (C) air-oxidized (D), and cyanide complex (E) forms of DosS GAF-A. Mol-A is shown in each of the asymmetric units of the five crystals.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 13057-13067) copyright 2009.

Figures were selected by an automated process.