Crystal structures of the key anaerobic enzyme pyruvate: Ferredoxin oxidoreductase, free and in complex with pyruvate
ABSTRACT Oxidative decarboxylation of pyruvate to form acetyl-coenzyme A, a crucial step in many metabolic pathways, is carried out in most aerobic organisms by the multienzyme complex pyruvate dehydrogenase. In most anaerobes, the same reaction is usually catalyzed by a single enzyme, pyruvate:ferredoxin oxidoreductase (PFOR). Thus, PFOR is a potential target for drug design against certain anaerobic pathogens. Here, we report the crystal structures of the homodimeric Desulfovibrio africanus PFOR (data to 2.3 A resolution), and of its complex with pyruvate (3.0 A resolution). The structures show that each subunit consists of seven domains, one of which affords protection against oxygen. The thiamin pyrophosphate (TPP) cofactor and the three [4Fe-4S] clusters are suitably arranged to provide a plausible electron transfer pathway. In addition, the PFOR-pyruvate complex structure shows the noncovalent fixation of the substrate before the catalytic reaction.
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- "produce a second molecule of oxaloacetate, completing the network-autocatalytic topology and making the cycle selfamplifying . The distinctive reaction in the rTCA pathway is a carbonyl insertion at a thioester (acetyl-CoA or succinyl-CoA), performed by a family of conserved ferredoxin-dependent oxidoreductases which are triple-Fe 4 S 4 -cluster proteins . "
ABSTRACT: Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Physical Biology 12/2012; 10(1):011001. DOI:10.1088/1478-3975/10/1/011001 · 3.14 Impact Factor
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- "The X-ray crystal structure of the A 2 -type pyruvate:ferredoxin oxidoreductase from Desulfovibrio africanus has been determined byChabrì ere et al.   and shown to contain one thiamine pyrophosphate, one Mg 2+ , and three [4Fe-4S] clusters as prosthetic groups per protomer . The ab-/a 2 b 2 -type homologs from aerobic archaea inherently lack the Fe-S subunit/domain called δ, which harbors two [4Fe-4S] clusters  , presumably as an evolutionary consequence of one protein adaptation strategy occurring under permanently oxidative conditions. "
ABSTRACT: The general importance of the Fe-S cluster prosthetic groups in biology is primarily attributable to specific features of iron and sulfur chemistry, and the assembly and interplay of the Fe-S cluster core with the surrounding protein is the key to in-depth understanding of the underlying mechanisms. In the aerobic and thermoacidophilic archaea, zinc-containing ferredoxin is abundant in the cytoplasm, functioning as a key electron carrier, and many Fe-S enzymes are produced to participate in the central metabolic and energetic pathways. De novo formation of intracellular Fe-S clusters does not occur spontaneously but most likely requires the operation of a SufBCD complex of the SUF machinery, which is the only Fe-S cluster biosynthesis system conserved in these archaea. In this paper, a brief introduction to the buildup and maintenance of the intracellular Fe-S world in aerobic and hyperthermoacidophilic crenarchaeotes, mainly Sulfolobus, is given in the biochemical, genetic, and evolutionary context.Archaea 09/2010; 2010. DOI:10.1155/2010/842639 · 2.03 Impact Factor
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- "Reduction of the protein with dithioerythritol or deletion of the C-terminal extension resulted in a protein with increased sensitivity to oxygen and increased activity (Pieulle et al., 1997). Analysis of the crystal structure confirmed the presence of a disulfide bond between the two cysteines of the C-terminal extension which blocks access to the proximal [4Fe–4S] cluster (Chabriere et al., 1999). "
ABSTRACT: Several cellular pathways have been identified which affect the efficiency of thiamine biosynthesis in Salmonella enterica. Mutants defective in iron-sulfur (Fe-S) cluster metabolism are less efficient at synthesis of the pyrimidine moiety of thiamine. These mutants are compromised for the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P), not the synthesis of AIR. The gene product ThiC contains potential ligands for an Fe-S cluster that are required for function in vivo. The conversion of AIR to HMP-P is sensitive to oxidative stress, and variants of ThiC have been identified that have increased sensitivity to oxidative growth conditions. The data are consistent with ThiC or an as-yet-unidentified protein involved in HMP-P synthesis containing an Fe-S cluster required for its physiological function.Microbiology 09/2006; 152(Pt 8):2345-53. DOI:10.1099/mic.0.28926-0 · 2.84 Impact Factor