1Y28

Crystal structure of the R220A metBJFIXL HEME domain

Summary for 1Y28

• Entry DOI: 10.2210/pdb1y28/pdb
• Related: 1D06 1DP6 1DP8 1DP9 1DRM 1LSV
• Descriptor: Sensor protein fixL, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: pas fold, oxygen sensing, transferase
• Biological source: Bradyrhizobium japonicum
• Total number of polymer chains: 1
• Total formula weight: 15450.23

Authors

Dunham, C.M.,Dioum, E.M.,Tuckerman, J.R.,Gonzalez, G.,Scott, W.G.,Gilles-Gonzalez, M.A. (deposition date: 2004-11-21, release date: 2004-12-07, Last modification date: 2023-10-25)

Primary citation

Dunham, C.M.,Dioum, E.M.,Tuckerman, J.R.,Gonzalez, G.,Scott, W.G.,Gilles-Gonzalez, M.A.
A distal arginine in the oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure
Biochemistry, 42:7701-7708, 2003

PubMed Abstract: To evaluate the contributions of the G(beta)-2 arginine to signal transduction in oxygen-sensing heme-PAS domains, we replaced this residue with alanine in Bradyrhizobium japonicum FixL and examined the results on heme-domain structure, ligand binding, and kinase regulation. In the isolated R220A BjFixL heme-PAS domain, the iron-histidine bond was increased in length by 0.31 A, the heme flattened even without a ligand, and the interaction of a presumed regulatory loop (the FG loop) with the helix of heme attachment was weakened. Binding of carbon monoxide was similar for ferrous BjFixL and R220A BjFixL. In contrast, the level of binding of oxygen was dramatically lower (K(d) approximately 1.5 mM) for R220A BjFixL, and this was manifested as 60- and 3-fold lower on- and off-rate constants, respectively. Binding of cyanide followed the same pattern as binding of oxygen. The catalytic activity was 3-4-fold higher in the "on-state" unliganded forms of R220A BjFixL than in the corresponding BjFixL species. Cyanide regulation of this activity was strongly impaired, but some inhibition was nevertheless preserved. Carbon monoxide and nitric oxide regulation, although weak in BjFixL, were abolished from R220A BjFixL. We conclude that the G(beta)-2 arginine assists in the binding of oxygen to BjFixL but does not accomplish this by stabilizing the oxy form. This arginine is not absolutely required for regulation, although it is important for shifting a pre-existing kinase equilibrium toward the inactive state on binding of regulatory ligands. These findings support a regulatory model in which the heme-PAS domain operates as an ensemble that couples to the kinase rather than a mechanism driven by a single central switch.

PubMed: 12820879
DOI: 10.1021/bi0343370

Experimental method

X-RAY DIFFRACTION (2.1 Å)