Structure of the redox sensor domain of Methylococcus capsulatus (Bath) MmoS

Abstract

MmoS from Methylococcus capsulatus (Bath) is the multidomain sensor protein of a two-component signaling system proposed to play a role in the copper-mediated regulation of soluble methane monooxygenase (sMMO). MmoS binds an FAD cofactor within its N-terminal tandem Per-Arnt-Sim (PAS) domains, suggesting that it functions as a redox sensor. The crystal structure of the MmoS tandem PAS domains, designated PAS-A and PAS-B, has been determined to 2.34 A resolution. Both domains adopt the typical PAS domain alpha/beta topology and are structurally similar. The two domains are linked by a long alpha helix and do not interact with one another. The FAD cofactor is housed solely within PAS-A and is stabilized by an extended hydrogen bonding network. The overall fold of PAS-A is similar to those of other flavin-containing PAS domains, but homodimeric interactions in other structures are not observed in the MmoS sensor, which crystallized as a monomer. The structure both provides new insight into the architecture of tandem PAS domains and suggests specific residues that may play a role in MmoS FAD redox chemistry and subsequent signal transduction.

Figure 1

Predicted domain organization of MmoS. The two PAS-PAC domains (labeled PAS-A and PAS-B) are followed by a GAF domain. The HATPase domain likely catalyzes phosphorylation of a histidine in the HisKA domain. The receiver domains (REC) and His-containing phosphotransfer domain may function in phosphate transfer to the partner regulator protein MmoQ.

Figure 2

Arrangement of the tandem PAS domains in (A) MmoS and (B) dPER (PDB accession code 1WA9). PAS-A is shown in blue, the linker region is shown in yellow, and PAS-B is shown in raspberry. The secondary structure elements are labeled for MmoS and the FAD cofactor is shown as sticks.

Figure 3

Stereo view of the FAD cofactor in PAS-A and interacting residues. Residues from PAS-A have blue carbon atoms, residues from PAS-B have raspberry carbon atoms, and the FAD has green carbon atoms. Nitrogen atoms are blue, oxygen atoms are red, sulfur atoms are yellow, and phosphorus atoms are orange. Water molecules are shown as red spheres. An omit electron density map of the FAD contoured at 3σ is superimposed.

Figure 4

Comparison of MmoS PAS domains to other PAS domains. (A) Superposition of PAS-A (blue), PAS-B (red), A. vinelandii NifL (yellow, PDB accession code 2GJ3), C. reinhardtii LOV1 (green, 1N9O), phy3 LOV2 (magenta, 1JNU), E. coli27DosH (black, 1V9Z), and B. japonicum FixLH (gray, 1XJ6). The FAD cofactor in PAS-A is shown as blue sticks. The heme cofactors in DosH and FixLH are not shown. (B) Structure based sequence alignment of structures shown in (A). Identical residues are highlighted green and similar residues are highlighted magenta. The secondary structure elements for MmoS PAS-A are indicated.

Figure 5

Crystal packing interactions between symmetry related monomers. The PAS-A domain in the middle interacts with the PAS-B domains from two different symmetry related molecules via interface 1 and interface 2.