A protein carboxylate coordinated oxo‐centered tri‐nuclear iron complex with possible implications for ferritin mineralization

Högbom, Martin; Nordlund, P.

doi:10.1016/j.febslet.2004.04.068

Cited by 13 publications

(10 citation statements)

References 21 publications

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“…Högdom and Nordlund reported the X-ray crystal structure of a protein-carboxylate-coordinated, oxo-centered, tri-nuclear iron cluster, which is formed on the surface of the ribonucleotide reductase R2 protein from Corynebacterium ammoniagenes during Fe 2+ uptake of the protein from solution. [37] This natural iron complex bears some structural resemblance to complex 10, i.e. the central Fe 3 (µ 3 -O) unit, the bridging carboxylate ligands, and the axial coordination site is occupied by a water molecule.…”

Section: Discussionmentioning

confidence: 99%

Syntheses, Crystal Structures, Spectroscopic Properties, and Catalytic Aerobic Oxidations of Novel Trinuclear Non‐Heme Iron Complexes

et al. 2009

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Keywords: Carboxylate ligands / EPR spectroscopy / EXAFS spectroscopy / Mössbauer spectroscopy / OxidationA series of 2,6-diacylpyridine ligand precursors 5a-d·HCl with different tether lengths between the carboxyl and pyridine moiety was prepared and converted into the correspondig trinuclear Fe 3 (µ 3 -O) complexes 8a-d and 10. Under slow precipitation conditions a tetranuclear complex 9 was isolated instead of 8a. Single-crystal X-ray diffraction analyses were performed on ligands 5a-d and complexes 9 and 10. Characterization by X-ray absorption spectroscopy (XAS) proved a trinuclear Fe 3 (µ 3 -O) core for complexes 8a-d. When complex 8a was submitted to Gif-type oxidations (O 2 , Zn, pyridine, HOAc), Mössbauer and nuclear inelastic scattering (NIS) suggested the formation of mononuclear species. The trinuclear ferric complex 10 has an isosceles molecular structure, which is manifested in the 57 Fe Mössbauer spectrum

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Section: Discussionmentioning

confidence: 99%

Syntheses, Crystal Structures, Spectroscopic Properties, and Catalytic Aerobic Oxidations of Novel Trinuclear Non‐Heme Iron Complexes

et al. 2009

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“…Although this difference density was modeled as an acetate ion, no acetate ion was used during purification and crystallization steps, and we are not sure about the actual identity of this difference density. A similar example for this modeling is the crystal structure of a ribonucleotide reductase R2 protein complexed with an oxo-centered trinuclear iron cluster, in which an acetate ion was found to coordinate two of the irons in the oxo-centered trinuclear iron cluster (18). Besides the modeled acetate group and protein residues, seven water molecules were also found to be involved in the coordination of the trinuclear iron cluster, with one water binding to Fe-5 and three waters each binding to Fe-6 and -7.…”

Section: Resultsmentioning

confidence: 99%

“…The fact that a multinuclear iron cluster is coordinated by an EXXXD motif pair has never been described previously. However, an oxo-centered trinuclear iron cluster coordinated by protein-derived carboxylates has been structurally characterized in the ribonucleotide reductase R2 protein, although these carboxyl residues are not conserved (18). In ferritins, the formation of an iron core is crucial for iron storage, detoxification, and mobilization throughout all three kingdoms.…”

Section: Discussionmentioning

confidence: 99%

Crystal Structure of a PhoU Protein Homologue

Liu

Lou

Yokota

et al. 2005

Journal of Biological Chemistry

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PhoU proteins are known to play a role in the regulation of phosphate uptake. In Thermotoga maritima, two PhoU homologues have been identified bioinformatically. Here we report the crystal structure of one of the PhoU homologues at 2.0 Å resolution. The structure of the PhoU protein homologue contains a highly symmetric new structural fold composed of two repeats of a three-helix bundle. The structure unexpectedly revealed a trinuclear and a tetranuclear iron cluster that were found to be bound on the surface. Each of the two multinuclear iron clusters is coordinated by a conserved E(D)XXXD motif pair. Our structure reveals a new class of metalloprotein containing multinuclear iron clusters. The possible functional implication based on the structure are discussed.Inorganic phosphate (P i ) uptake is of fundamental importance in the cell physiology of bacteria because P i is required as a nutrient. Escherichia coli has developed a P i acquisition system that allows the assimilation of P i via a variety of systems. Two distinct systems for the uptake of P i have been described: the low affinity phosphate inorganic transporter and the high affinity phosphate-specific transporter (PstSCAB) (1, 2). When the preferred P i source is in excess, it is taken up by the phosphate inorganic transporter. When the extracellular P i concentration is less than ϳ4 M, the synthesis of the high affinity transporter is induced, and P i is taken up by PstSCAB. The PstSCAB transporter belongs to the superfamily of ATPbinding cassette transporters and is encoded by the pst operon (3, 4). This operon contains five genes that are transcribed counterclockwise in the following order: pstS, pstC, pstA, pstB, and phoU. PstS is a periplasmic P i -binding protein, and PstC and PstA are integral membrane proteins that mediate the translocation of P i through the inner membrane. PstB is an ATPase that energizes the transport. The Pst operon is part of the phosphate (PHO) 1 regulon that consists of 31 genes arranged in eight different operons in E. coli (5, 6). The genes and operons of the PHO regulon are co-regulated by a two-component system composed of the regulatory proteins PhoB and PhoR. When the concentration of P i in the medium falls below ϳ4 M, the sensor protein PhoR phosphorylates PhoB, and the phosphorylated PhoB binds to the PHO boxes in the control region of Pst, recruiting the 70 subunit of the RNA polymerase and initiating transcription. When the P i concentration in the medium is in excess, the PHO regulon is repressed. Repression of the PHO regulon requires not only an excess concentration of extracellular P i but also the intact PstSCAB transporter and the PhoU protein.The PhoU gene encodes a polypeptide of molecular mass ϳ27,000 Da. Although it is located in the pst operon, the encoded PhoU protein does not seem to participate in P i transport (4). Besides its role as a repressor of the PHO regulon, PhoU was also reported to be involved in intracellular P i metabolism (presumably related to the synthesis of ATP) (7).Currently...

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“…The observed L-ferritin trinuclear cluster can be considered as a portion of the hexanuclear synthetic cluster discussed in Results, which was proposed to represent a ferritin biomineral model (15). Other authors have suggested that an oxo-centered trinuclear iron cluster, which forms spontaneously on the surface of class Ib ribonucleotide reductase R2 protein from Corynebacterium ammoniagenes in crystals subjected to iron soaking, could mimic an early stage in the mineralization of iron in ferritins (23). In this case, however, the bridging ligands were provided by six carboxylates whereas no peroxide anions were detected (23).…”

Section: Discussionmentioning

confidence: 99%

Chemistry at the protein–mineral interface in L-ferritin assists the assembly of a functional (μ ³ -oxo)Tris[(μ ² -peroxo)] triiron(III) cluster

Pozzi

Ciambellotti

Bernacchioni

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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X-ray structures of homopolymeric L-ferritin obtained by freezing protein crystals at increasing exposure times to a ferrous solution showed the progressive formation of a triiron cluster on the inner cage surface of each subunit. After 60 min exposure, a fully assembled (μ 3 -oxo)Tris[(μ 2 -peroxo)(μ 2 -glutamato-κO:κO′)](glutamato-κO)(diaquo)triiron(III) anionic cluster appears in human L-ferritin. Glu60, Glu61, and Glu64 provide the anchoring of the cluster to the protein cage. Glu57 shuttles incoming iron ions toward the cluster. We observed a similar metallocluster in horse spleen L-ferritin, indicating that it represents a common feature of mammalian L-ferritins. The structures suggest a mechanism for iron mineral formation at the protein interface. The functional significance of the observed patch of carboxylate side chains and resulting metallocluster for biomineralization emerges from the lower iron oxidation rate measured in the E60AE61AE64A variant of human L-ferritin, leading to the proposal that the observed metallocluster corresponds to the suggested, but yet unobserved, nucleation site of L-ferritin.L-ferritin | metallocluster | nucleation site | biomineralization | X-ray

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A protein carboxylate coordinated oxo‐centered tri‐nuclear iron complex with possible implications for ferritin mineralization

Cited by 13 publications

References 21 publications

Syntheses, Crystal Structures, Spectroscopic Properties, and Catalytic Aerobic Oxidations of Novel Trinuclear Non‐Heme Iron Complexes

Syntheses, Crystal Structures, Spectroscopic Properties, and Catalytic Aerobic Oxidations of Novel Trinuclear Non‐Heme Iron Complexes

Crystal Structure of a PhoU Protein Homologue

Chemistry at the protein–mineral interface in L-ferritin assists the assembly of a functional (μ ³ -oxo)Tris[(μ ² -peroxo)] triiron(III) cluster

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A protein carboxylate coordinated oxo‐centered tri‐nuclear iron complex with possible implications for ferritin mineralization

Cited by 13 publications

References 21 publications

Syntheses, Crystal Structures, Spectroscopic Properties, and Catalytic Aerobic Oxidations of Novel Trinuclear Non‐Heme Iron Complexes

Syntheses, Crystal Structures, Spectroscopic Properties, and Catalytic Aerobic Oxidations of Novel Trinuclear Non‐Heme Iron Complexes

Crystal Structure of a PhoU Protein Homologue

Chemistry at the protein–mineral interface in L-ferritin assists the assembly of a functional (μ 3 -oxo)Tris[(μ 2 -peroxo)] triiron(III) cluster

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Chemistry at the protein–mineral interface in L-ferritin assists the assembly of a functional (μ ³ -oxo)Tris[(μ ² -peroxo)] triiron(III) cluster