A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans

Abstract

Reactions involving the fixation of carbon monoxide (CO) into activated acetyl groups on surfaces containing the sulfides of nickel and iron have been implicated in models of the chemoautotrophic origin of life (1, 2). These models adopt sequences of the acetyl-CoA pathway (Wood͞Ljungdahl pathway), which is operative in CO 2 fixation by autotrophic acetogens, sulfidogens, and methanogens, as well as in acetate utilization by methanogens (3-7). The synthesis of acetyl-CoA in the pathway involves the functions of a NiFeS acetyl-CoA synthase (ACS), a NiFeS CO dehydrogenase (CODH), and a cobalt-containing corrinoid iron-sulfur protein (CoFeSP). ACS and CODH form a tight complex in all microorganisms that have been previously examined in that respect (4-6). ACS catalyzes the synthesis of acetyl-CoA from a methyl group donated by CoFeSP, CO, and CoA (Eq. 1) (5, 6). CODH catalyzes the reduction of CO 2 to CO, which reappears in the carboxyl group of the acetyl residue formed (Eq. 2) (5, 6).Carboxydothermus hydrogenoformans is a hydrogenogenic bacterium that utilizes CO as a sole source of carbon and energy under anaerobic chemolithoautotrophic conditions (8). The bacterium presumably employs the acetyl-CoA pathway for the assimilation of carbon (V.S., personal communication). The genomic sequence of C. hydrogenoformans contains an Ϸ10-kb region that assembles the predicted functions of the genes cooSIII (CODHIII Ch , 73.3 kDa), acs (ACS, 82.2 kDa), cfsA and cfsB (the 48.8-kDa large and the 33.9-kDa small subunits of the heterodimeric CoFeSP), and mtr (a 29.3-kDa methyltransferase) (Fig. 1A). The deduced amino acid sequence of acs from C. hydrogenoformans shows 74% identity (86% similarity) to the complexed ACS Mt from Moorella thermoacetica (9).According to a recent model (9), the generation of energy and reducing equivalents in C. hydrogenoformans involves the activities of the monofunctional CODHI Ch and CODHII Ch . A first crystal structure of a NiFeS-CODH, the CODHII Ch , at 1.6 Å resolution in the dithionite-reduced state showed five metal clusters, of which clusters B, BЈ, and a subunit-bridging, surface-exposed cluster D are cubane-type [4Fe-4S] clusters (10). The active-site clusters C and CЈ are asymmetric [Ni-4Fe-5S] clusters. Their integral Ni ion, which is the likely site of CO oxidation, is coordinated by four sulfur ligands with square planar geometry. The CODH Rr crystal structure from Rhodospirillum rubrum determined at 2.8-Å resolution shows a similar overall structure, except that cluster C is interpreted as a [Ni-3Fe-4S] cubane, to which a mononuclear Fe site is coordinated (11). Cluster C in the CODH component of the ACS Mt ͞CODH Mt complex from M. thermoacetica has been described as a Ni-4Fe-4S cage that can be viewed as a [Ni-Fe] Doukov et al. (13) and Darnault et al. (12) are generally similar and have an ␣ 2 ␤ 2 (␣, ACS; ␤, CODH) quaternary structure. The structures of the CODH Mt subunits are similar in the two crystal forms and closely resemble the structures of CODHII Ch (10) and CODH R...

The rocky roots of the acetyl-CoA pathway

“…Notably, the reaction is more exergonic at low temperatures than at high temperatures [39]. nickel in a novel Ni-Ni-[4Fe4S] cluster [18]. CODH and ACS can occur together as a single bifunctional enzyme (ACS -CODH) or as separate, monofunctional enzymes [19,20].…”

“…The structures of a C-cluster in CODH and of the A-cluster of ACS (Figure 2a [16][17][18][19][20]35]. The exact reaction mechanism for ACS has not been resolved: differing proposals have been put forth [17,20] and differences have been also reported regarding the presence of copper, zinc and nickel at the active site of the A cluster [17,20,35]; nickel has been found at the active site of the active enzyme [18]. Only selected metal sulphide centres of CODH and ACS are shown; the protein structure is represented by shading.…”

Structural insights into methyltransfer reactions of a corrinoid iron–sulfur protein involved in acetyl-CoA synthesis

“…hydrogenoformans can use CO as a sole source of energy and carbon under anaerobic chemolithoautotrophic conditions. Protons serve as terminal electron acceptor (7), and the methyl branch of the acetyl-CoA pathway is used for the assimilation of carbon (6). The oxidation of CO in this bacterium is catalyzed by two monofunctional NiFe-containing CODHs (CODHI Ch and CODHII Ch ) that harbor the [Ni-4Fe-5S] active site cluster C (7).…”

“…CoFeSP has been isolated and characterized from the acetogenic bacterium Moorella thermoacetica (4), the methanogenic archaeon Methanosarcina thermophila (5), and the hydrogenogenic bacterium Carboxydothermus hydrogenoformans (6).…”

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe–4S] cluster

“…The existence of different types of [Fe-S] proteins and clusters points to a remarkable functional and structural diversity, reflecting the chemical versatility of both iron and sulfur [3,4]. The known functions of biological [Fe-S] clusters include electron transfer in Fds and redox enzymes [1,[5][6][7], coupled electron/proton transfer [8], substrate binding and activation [9][10][11][12][13][14][15][16][17][18][19], Fe or cluster storage [20], structural control [21][22][23], regulation of gene expression [24][25][26][27][28][29][30][31] and enzyme activity [32][33][34], disulfide reduction [35][36][37] and sulfur donation [38][39][40].…”