PDBsum entry 1d06

Signaling protein

PDB id: 1d06

Contents

Protein chain

130 a.a. *

Ligands

HEM

Waters ×73

* Residue conservation analysis

PDB id:

1d06

Name:

Signaling protein

Title:

Structural basis of dimerization and sensory mechanisms of oxygen- sensing domain of rhizobium meliloti fixl determined at 1.4a resolution

Structure:

Nitrogen fixation regulatory protein fixl. Chain: a. Engineered: yes. Mutation: yes

Source:

Sinorhizobium meliloti. Organism_taxid: 382. Expressed in: escherichia coli k12. Expression_system_taxid: 83333.

Biol. unit:

Dimer (from PQS)

Resolution:

1.40Å R-factor: 0.224 R-free: 0.275

Authors:

H.Miyatake,M.Mukai,S.-Y.Park,S.Adachi,K.Tamura,H.Nakamura,K.Nakamura, T.Tsuchiya,T.Iizuka,Y.Shiro

Key ref:

H.Miyatake et al. (2000). Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies. J Mol Biol, 301, 415-431. PubMed id: 10926518 DOI: 10.1006/jmbi.2000.3954

Date:

09-Sep-99 Release date: 15-Mar-00

Protein chain

P10955  (FIXL_RHIME) -  Sensor protein FixL from Rhizobium meliloti (strain 1021)

Seq: 505 a.a.

Struc: 130 a.a.*

* PDB and UniProt seqs differ at 6 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: 10.1006/jmbi.2000.3954

J Mol Biol 301:415-431 (2000)

PubMed id: 10926518

Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies.

H.Miyatake, M.Mukai, S.Y.Park, S.Adachi, K.Tamura, H.Nakamura, K.Nakamura, T.Tsuchiya, T.Iizuka, Y.Shiro.

ABSTRACT

FixL of Rhizobium meliloti (RmFixL) is a sensor histidine kinase of the two-component system, which regulates the expression of the genes related to nitrogen fixation in the root nodule in response to the O(2) levels. The crystal structure of the sensor domain of FixL (RmFixLH), which contains a heme (Fe-porphyrin) as a sensing site, was determined at 1.4 A resolution. Based on the structural and spectroscopic analyses, we propose the O(2) sensing mechanism that differs from the case proposed in BjFixLH as follows; conformational changes in the F/G loop, which are induced by steric repulsion between the bent-bound O(2) and the Ile209 side-chain, would be transmitted to the histidine kinase domain. Interaction between the iron-bound O(2) and Ile209 was also observed in the resonance Raman spectra of RmFixLH as evidenced by the fact that the Fe-O(2) and Fe-CN stretching frequencies were shifted from 575 to 570 cm(-1) (Fe-O(2)), and 504 to 499 cm(-1), respectively, as the result of the replacement of Ile209 with an Ala residue. In the I209A mutant of RmFixL, the O(2) sensing activity was destroyed, thus confirming our proposed mechanism.

Selected figure(s)

Figure 3.
Figure 3. Dimerization interaction at the N-terminal: (a) "Leucine-zipper"-like interaction at helix II with CPK representations. (b) The interaction between helix I and the RmFixLH core region. The pictures (a) and (b) were depicted with MOLSCRIPT and RASTER3D. (c) The amino acid sequences of the leucine zipper-like helices (helix II) of Rhizobium meliloti (RmFixLH), Bradyrhizobium japonicum (BjFixLH) and Azorhizobium caulinodans (AcFixLH) are drawn in a-helical wheels, in order to present the amphipathic nature, in which hydrophobic residues are colored in yellow, while the others are in light blue.

Figure 6.
Figure 6. (a) Heme and its surroundings with distances (Å) and electron density map (>1s). Distal side residues (Ile209, Ile210, Leu230, Val232) and proximal residues (His194, Asn181, Asp195) are shown. (b) Top and side views of a van der Waals drawing of the structure at the heme distal region.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 415-431) copyright 2000.

Figures were selected by an automated process.