Structure of C42D Azotobacter vinelandii FdI

Jung, Yean-Sung; Bonagura, Christopher A.; Tilley, Gareth J.; Gao-Sheridan, H. Samantha; Armstrong, Fräser A.; Stout, C.D.; Burgess, Barbara K.

doi:10.1074/jbc.m004947200

Cited by 23 publications

(15 citation statements)

References 95 publications

(36 reference statements)

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“…The predicted amino acid sequence of the TcuB protein (379 aa, 42 kDa) has some interesting features. The N-terminal region of the protein displayed two distinct cysteine motifs that matched the consensus C-X 2 -C-X 2 -C-X 3 -C-X sequence found in proteins with iron-sulfur centers (21). These motifs are located at residues 28 to 38 and 62 to 72 in the TcuB sequence (Fig.…”

Section: Resultsmentioning

confidence: 99%

The Tricarballylate Utilization ( tcuRABC ) Genes of Salmonella enterica Serovar Typhimurium LT2

et al. 2004

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The genes of Salmonella enterica serovar Typhimurium LT2 encoding functions needed for the utilization of tricarballylate as a carbon and energy source were identified and their locations in the chromosome were established. Three of the tricarballylate utilization (tcu) genes, tcuABC, are organized as an operon; a fourth gene, tcuR, is located immediately 5 to the tcuABC operon. The tcuABC operon and tcuR gene share the same direction of transcription but are independently transcribed. The tcuRABC genes are missing in the Escherichia coli K-12 chromosome. The tcuR gene is proposed to encode a regulatory protein needed for the expression of tcuABC. The tcuC gene is proposed to encode an integral membrane protein whose role is to transport tricarballylate across the cell membrane. tcuC function was sufficient to allow E. coli K-12 to grow on citrate (a tricarballylate analog) but not to allow growth of this bacterium on tricarballylate. E. coli K-12 carrying a plasmid with wild-type alleles of tcuABC grew on tricarballylate, suggesting that the functions of the TcuABC proteins were the only ones unique to S. enterica needed to catabolize tricarballylate. Analyses of the predicted amino acid sequences of the TcuAB proteins suggest that TcuA is a flavoprotein, and TcuB is likely anchored to the cell membrane and probably contains one or more Fe-S centers. The TcuB protein is proposed to work in concert with TcuA to oxidize tricarballylate to cis-aconitate, which is further catabolized via the Krebs cycle. The glyoxylate shunt is not required for growth of S. enterica on tricarballylate. A model for tricarballylate catabolism in S. enterica is proposed.Tricarballylate (1,2,3-propanetricarboxylate) is structurally related to citric acid; hence, its catabolism is thought to proceed via the tricarboxylic acid (Krebs) cycle (Fig. 1). Tricarballylate is the causative agent of grass tetany, a disease in ruminants characterized by a pronounced magnesium ion deficiency. Reports in the literature have established a strong correlation between high levels of trans-aconitate (trans-1-propene-1,2,3-tricaboxylate) in the rumen with the incidence of the disease (6). In the rumen, trans-aconitate is rapidly converted to tricarballylate in a single reductive step (Fig. 2) (25). It is not clear how tricarballylate causes grass tetany; however, it is known that tricarballylate is a good chelator of magnesium ions and that it enhances excretion of this important divalent metal ion (33). In addition, tricarballylate is known to be a potent inhibitor of aconitase, a key enzyme of the Krebs cycle (26,29,33). This effect on aconitase makes tricarballylate particularly toxic to organisms that rely on the Krebs cycle for energy generation and are unable to catabolize tricarballylate into nontoxic metabolites.In the rumen, Selenomonas ruminantium is the primary producer of tricarballylate (25). Not surprisingly, this bacterium has been the target of studies aimed at blocking the accumulation of this compound. The bacterium Acidaminococcus ferm...

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Section: Resultsmentioning

confidence: 99%

The Tricarballylate Utilization ( tcuRABC ) Genes of Salmonella enterica Serovar Typhimurium LT2

et al. 2004

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“…3) are clearly in the gЈ ϭ 2.01 category, although a portion of the signal appears to be that of a radical. The narrow gЈ ϭ 2.01 cluster signals arise from [3Fe-4S] 1ϩ , a fact that has been established by comparison of several types of spectroscopy and x-ray structures for various preparations of aconitase (32,33) and the 3Fe center of 7-iron ferredoxins (35). For [4Fe-4S] clusters with only 3 iron-Cys bonds, as in aconitase, the fourth, Cys-free iron is the one lost.…”

Section: Discussionmentioning

confidence: 99%

“…The spectroscopic signatures of FeS clusters are well documented for numerous proteins and model compounds of determined structures (13,(32)(33)(34) (29,35).…”

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confidence: 99%

Redox Reactions of the Iron-Sulfur Cluster in a Ribosomal RNA Methyltransferase, RumA

Agarwalla

Stroud

Gaffney

2004

Journal of Biological Chemistry

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RumA, an S-adenosyl-L-methionine-dependent methyltransferase specifically catalyzes the methylation of U1939 of 23 S ribosomal RNA to yield 5-methyluridine (m 5 U) 1 or ribothymidine (1). This enzyme was found to contain a [4Fe-4S] cluster, a prosthetic group usually not associated with methyltransferase enzymes. The x-ray structure of RumA revealed that the cluster is located in the RNA binding domain of the threedomain protein (2). It is held by four Cys-iron bonds provided by Cys 81 , Cys 87 , Cys 90 , and Cys 162 and is buried in a largely hydrophobic region, but one of its sulfur atoms is quite exposed to solvent. The closest distance between the cluster and the sulfur of the catalytic nucleophile, Cys 389 , is ϳ19 Å. RumA is a member of a growing list of nucleic acid modifying enzymes where the function of the iron-sulfur (FeS) cluster remains enigmatic.The reaction mechanism of m 5 U methyltransferases is similar to that of thymidylate synthase, and has been studied mainly employing the tRNA m 5 U54 methyltransferase, TrmA (3-5). It involves Michael addition of the catalytic Cys to carbon 6 (C-6) of pyrimidine, which activates C-5 for a nucleophilic attack on the methyl group of S-adenosyl-L-methionine. Following the methyl transfer, the enzyme is resolved by abstraction of a proton from C-5 and ␤-elimination. TrmA, as well as DNA and RNA 5-methylcytidine methyltransferases, which employ a similar catalytic mechanism (6), do not posses an FeS cluster or any other prosthetic group. Lack of a redox step in the catalytic mechanism, and absence of the cluster in enzymes that employ a similar mechanism preclude a direct role for [4Fe-4S] cluster in the RumA-catalyzed reaction.Two features distinguish the FeS cluster in RumA from the clusters in a different class of S-adenosyl-L-methionine-dependent enzymes that proceed by free radical mechanisms. The RumA cluster is ligated by 4 cysteines and the iron-binding sequence motif is CX 5 CX 2 CX n C. In contrast, the radical Sadenosyl-L-methionine enzymes, of which MiaB (7) and biotin synthase (8) are examples, have a [4Fe-4S] cluster built of a CX 3 CX 2 C sequence that leaves one iron of the cluster free to participate in catalysis. MiaB is a member of a family of enzymes catalyzing addition of sulfur to tRNA bases (9). The FeS sequence motifs in the DNA repair enzymes, endonuclease III (10) and MutY (11), are CX 6 CX 2 CX 5 C, somewhat similar to the RumA sequence. Although the FeS clusters in these enzymes are usually regarded as structural, recently it was shown that the redox potential of MutY is altered by DNA binding and that a change in charge of the [4Fe-4S] 3ϩ/2ϩ cluster might alter its affinity for DNA (12).The redox potentials of [4Fe-4S] clusters vary widely (13-16). Of particular interest in many contemporary studies of FeS proteins is understanding the factors that influence the potentials, and thus functions, of these clusters (17,18). Proteins with four Cys-iron bonds to the [4Fe-4S] cluster fall into two general redox groups, ones with an accessib...

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“…The EPR experiments of the present study did not reveal evidence for high spin ground states of mutant proteins C35S, C35D, and C35D/S94C of (BchY/BchZ) 2 . These data might mirror the outcome of a mutant study for a four-cysteine-ligated cluster of a ferredoxin from A. vinelandii, which revealed the same S ϭ 1/2 spin signal before and after cysteine versus aspartate replacement (53).…”

Section: Discussionmentioning

confidence: 93%

Iron-Sulfur Cluster-dependent Catalysis of Chlorophyllide a Oxidoreductase from Roseobacter denitrificans

Kiesel

Wätzlich

Lange

et al. 2015

Journal of Biological Chemistry

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Background: Synthesis of bacteriochlorophylls is essential for the photosynthetic capture of solar energy. Results: Chlorophyllide a oxidoreductase (COR) performs nitrogenase-related redox catalysis using two cysteine-ligated [4Fe-4S] clusters. Conclusion: A reductive trans protonation mechanism and an identical substrate binding mode for nitrogenase-like enzymes was deduced. Significance: Energy transduction of COR is relevant for related systems involved in the reduction of chemically stable multibonds.

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Structure of C42D Azotobacter vinelandii FdI

Cited by 23 publications

References 95 publications

The Tricarballylate Utilization ( tcuRABC ) Genes of Salmonella enterica Serovar Typhimurium LT2

The Tricarballylate Utilization ( tcuRABC ) Genes of Salmonella enterica Serovar Typhimurium LT2

Redox Reactions of the Iron-Sulfur Cluster in a Ribosomal RNA Methyltransferase, RumA

Iron-Sulfur Cluster-dependent Catalysis of Chlorophyllide a Oxidoreductase from Roseobacter denitrificans

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