Structural insights into methyltransfer reactions of a corrinoid iron-sulfur protein involved in acetyl-CoA synthesis - PubMed (original) (raw)
Structural insights into methyltransfer reactions of a corrinoid iron-sulfur protein involved in acetyl-CoA synthesis
Tatiana Svetlitchnaia et al. Proc Natl Acad Sci U S A. 2006.
Abstract
The cobalt- and iron-containing corrinoid iron-sulfur protein (CoFeSP) is functional in the acetyl-CoA (Ljungdahl-Wood) pathway of autotrophic carbon fixation in various bacteria and archaea, where it is essential for the biosynthesis of acetyl-CoA. CoFeSP acts in two methylation reactions: the transfer of a methyl group from methyltransferase (MeTr)-bound methyltetrahydrofolate to the cob(I)amide of CoFeSP and the transfer of the methyl group of methyl-cob(III)amide to the reduced Ni-Ni-[4Fe-4S] active site cluster A of acetyl-CoA synthase (ACS). We have solved the crystal structure of as-isolated CoFeSP(Ch) from the CO-oxidizing hydrogenogenic bacterium Carboxydothermus hydrogenoformans at 1.9-A resolution. The heterodimeric protein consists of two tightly interacting subunits with pseudo-twofold symmetry. The large CfsA subunit comprises three domains, of which the N-terminal domain binds the [4Fe-4S] cluster, the middle domain is a (betaalpha)(8)-barrel, and the C-terminal domain shows an open fold and binds Cobeta-aqua-(5,6-dimethylbenzimidazolylcobamide) in a "base-off" state without a protein ligand at the cobalt ion. The small CfsB subunit also displays a (betaalpha)(8)-barrel fold and interacts with the upper side of the corrin macrocycle. Structure-based alignments show that both (betaalpha)(8)-barrel domains are related to the MeTr in the acetyl-CoA pathway and to the folate domain of methionine synthase. We suggest that the C-terminal domain of the large subunit is the mobile element that allows the necessary interaction of CoFeSP(Ch) with the active site of ACS(Ch) and the methyltetrahydrofolate carrying MeTr. The conformation in the crystal structure shields the two open coordinations of cobalt and likely represents a resting state.
Conflict of interest statement
The authors declare no conflict of interest.
Figures
Fig. 1.
Overall structure of CoFeSPCh from C. hydrogenoformans. (A) Stereo ribbon presentation of the CoFeSPCh structure. CfsA is shown with α-helices in red and β-sheets in yellow, and CfsB is shown with α-helices in cyan and β-sheets in magenta. Cba denotes the cobamide cofactor. The proline-rich linker connecting the middle and C-terminal domains of CfsA is blue and labeled as linker. Cofactors (corrinoid cofactor and [4Fe-4S] center) are presented as a ball-and-stick model (Co in wheat, C in light blue, O in red, N in dark blue, Fe in aquamarine, and S in dark yellow). (Inset) An anomalous difference Fourier map (red) around the [4Fe-4S] cluster, contoured at 3.0σ, is shown with the overall structure and magnified. (B) Ribbon presentation of CfsA and CfsB with the (βα)8-barrel domains in rainbow colors from the N termini in blue to the C termini in red. The C-terminal domain of CfsA is shown in magenta. Helices forming the four-helical bundle like arrangement in the subunit interface are labeled; a star denotes helices of CfsB. (C) Superimposition of CfsB (red) on CfsA (aquamarine). All pictures were prepared by using PyMol (26).
Fig. 2.
The corrinoid cofactor. (A) Ribbon representation of the C-terminal domain of CfsA with bound corrinoid cofactor. The cap-helix is aquamarine; otherwise, colors are as in Fig. 1_A_. An omit F_obs−_F_calc map for the ribose and dimethylbenzimidazol part of the cofactor is shown in light brown. (B) Schematic presentation of the corrin macrocycle and its interaction with the protein environment. The interacting residues are colored red if they belong to CfsA and blue if they are part of CfsB. Yellow ellipses mark residues with hydrophobic contacts to the β-side of the corrin macrocycle. (C) Stick presentation of amino acids near the corrinoid cofactor. Coloring of the cofactor as in Fig. 1_A. An omit map excluding all atoms of the corrin macrocycle and the water ligand from the calculation of the phase set used for the _F_obs−_F_calc synthesis is shown in blue; the contour level is 3σ. The ligand bound to the cobalt-β position is modeled as a water molecule shown as an orange sphere. (D) Superimposition of the cobalamin-binding domain of MetH (blue) and the C-terminal domain of CfsA (dark red).
Fig. 3.
Methyltransfer cycle of CoFeSPCh. (A) The methyltransfer and the inactivation/reactivation cycle of CoFeSPCh. (a–d) The different conformations and interactions of the protein during the catalytic cycle; “e donox” and “e donred” are used for the electron donor of the [4Fe-4S] cluster of CoFeSPCh in the oxidized and reduced state, and “e accox” and “e accred” are used for the unspecific electron acceptor of Cob(I) in the oxidized and reduced state. During the catalytic cycle, the protein cycles between CH3-Cob(III) and Cob(I). Methyltransfer reactions are from (d) CH3-H4folate to Cob(I) and (a) CH3-Cob(III) to the cluster A of ACSCh. (B) Hypothetical model for CoFeSPCh methyltransfer cycle. The model assumes the C-terminal domain of CfsA as the only mobile element and draws from the analogy to cobalamin-dependent methionine synthase. (a–d) The different states as used in A. For details, see Results and Discussion.
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