Structural characterization of an iron–sulfur cluster assembly protein IscU in a zinc‐bound form

Liu, Jinyu; Oganesyan, Natalia; Shin, Dongkun; Jancarik, J.; Yokota, Hisao; Kim, Rosalind; Kim, Sung Hou

doi:10.1002/prot.20421

Cited by 57 publications

(54 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our results suggest that the His tag, which is located immediately downstream of the metal-chelating cysteines, interferes with the stability of the iron center in YciM, leading to the replacement of iron by zinc. The low iron content of YciM Strep * and YciM * very likely results from the notoriously low stability of iron centers, which often leads to the replacement of iron by zinc during protein overexpression and purification (34)(35)(36). Importantly, we have demonstrated that this iron center is essential for YciM function although whether it plays a structural or redoxrelated role remains unknown.…”

Section: Discussionmentioning

confidence: 82%

Insights into the Function of YciM, a Heat Shock Membrane Protein Required To Maintain Envelope Integrity in Escherichia coli

Nicolaes¹,

Hajjaji²,

Davis³

et al. 2013

Journal of Bacteriology

View full text Add to dashboard Cite

The cell envelope of Gram-negative bacteria is an essential organelle that is important for cell shape and protection from toxic compounds. Proteins involved in envelope biogenesis are therefore attractive targets for the design of new antibacterial agents. In a search for new envelope assembly factors, we screened a collection of Escherichia coli deletion mutants for sensitivity to detergents and hydrophobic antibiotics, a phenotype indicative of defects in the cell envelope. Strains lacking yciM were among the most sensitive strains of the mutant collection. Further characterization of yciM mutants revealed that they display a thermosensitive growth defect on low-osmolarity medium and that they have a significantly altered cell morphology. At elevated temperatures, yciM mutants form bulges containing cytoplasmic material and subsequently lyse. We also discovered that yciM genetically interacts with envC, a gene encoding a regulator of the activity of peptidoglycan amidases. Altogether, these results indicate that YciM is required for envelope integrity. Biochemical characterization of the protein showed that YciM is anchored to the inner membrane via its N terminus, the rest of the protein being exposed to the cytoplasm. Two CXXC motifs are present at the C terminus of YciM and serve to coordinate a redox-sensitive iron center of the rubredoxin type. Both the N-terminal membrane anchor and the C-terminal iron center of YciM are important for function.A ntibiotic resistance has become a worldwide problem that threatens the effectiveness of many medicines used today to treat bacterial infections. A particularly serious threat is the emergence of Gram-negative pathogens, including Escherichia coli and Pseudomonas aeruginosa, which are resistant to all of the available antibacterial agents (1). It is therefore urgent to develop new antibiotics active against Gram-negative bacteria, which requires a deep understanding of the biology of these organisms. Proteins playing a role in the assembly of the cell envelope are attractive targets for antibiotic development because this structure is essential for viability and protection against toxic compounds such as antibiotics.The envelope of Gram-negative bacteria is characterized by the presence of two concentric membranes, the inner membrane (IM) and outer membrane (OM), which are separated by the periplasm, a compartment that represents between 10 and 20% of the total cell volume and contains the peptidoglycan layer, or sacculus (2-4). The peptidoglycan sacculus is a heteropolymeric macromolecule composed of relatively short glycan strands and peptide cross-links, which serve to maintain cell morphology and give protection from turgor pressure. Although several proteins that play a key role in the biogenesis of the cell envelope have been identified recently (5-7), we have a poor understanding of how this complex architecture is assembled and of how envelope biogenesis is coordinated with cell growth and division. For instance, we do not know how the phospholipids that ...

show abstract

Section: Discussionmentioning

confidence: 82%

Insights into the Function of YciM, a Heat Shock Membrane Protein Required To Maintain Envelope Integrity in Escherichia coli

Nicolaes¹,

Hajjaji²,

Davis³

et al. 2013

Journal of Bacteriology

View full text Add to dashboard Cite

show abstract

“…The structures of the monomeric IscU apo form from Haemophilus influenzae (Hi) 25 and Mus musculus (Mm) and of SufU from Bacillus subtilis (Bs) and Streptococcus pyogenes (Sp) 26 have so far been determined. These structures contain a highly conserved α + β globular core architecture, but, intriguingly, the conformations of the N-terminal segments are quite variable.…”

Section: Introductionmentioning

confidence: 99%

The Asymmetric Trimeric Architecture of [2Fe–2S] IscU: Implications for Its Scaffolding during Iron–Sulfur Cluster Biosynthesis

Shimomura

Wada

Fukuyama

et al. 2008

Journal of Molecular Biology

120

View full text Add to dashboard Cite

“…The early structural studies of IscU were of its complex with Zn 2+ (Table 1). These structures showed that the three conserved cysteine residues (C37, C63, and C106) coordinate the metal, but the fourth ligand was reported differently in X-ray structures as the conserved D39 [75,76] or in an NMR structure as the conserved H105 [77]. The X-ray structures of [2Fe–2S]:IscU [78] and the [2Fe–2S]:IscU–IscS complex [68] showed the ligands as C37, C63, H105, and C106 (in the E. coli numbering system); however, the more stable IscU variant D39A was used in both studies, which eliminated this potential ligand.…”

Section: Introductionmentioning

confidence: 99%

Tangled web of interactions among proteins involved in iron–sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies

Kim

Bothe

Alderson

et al. 2015

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research

View full text Add to dashboard Cite

Proteins containing iron–sulfur (Fe–S) clusters arose early in evolution and are essential to life. Organisms have evolved machinery consisting of specialized proteins that operate together to assemble Fe–S clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. To date, the best studied system is the iron sulfur cluster (isc) operon of Escherichia coli, and the eight ISC proteins it encodes. Our investigations over the past five years have identified two functional conformational states for the scaffold protein (IscU) and have shown that the other ISC proteins that interact with IscU prefer to bind one conformational state or the other. From analyses of the NMR spectroscopy-derived network of interactions of ISC proteins and small-angle X-ray scattering (SAXS), chemical crosslinking experiments, and functional assays, we have constructed working models for Fe–S cluster assembly and delivery. Future work is needed to validate and refine what has been learned about the E. coli system and to extend these findings to the homologous Fe–S cluster biosynthetic machinery of yeast and human mitochondria. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

show abstract

Structural characterization of an iron–sulfur cluster assembly protein IscU in a zinc‐bound form

Cited by 57 publications

References 28 publications

Insights into the Function of YciM, a Heat Shock Membrane Protein Required To Maintain Envelope Integrity in Escherichia coli

Insights into the Function of YciM, a Heat Shock Membrane Protein Required To Maintain Envelope Integrity in Escherichia coli

The Asymmetric Trimeric Architecture of [2Fe–2S] IscU: Implications for Its Scaffolding during Iron–Sulfur Cluster Biosynthesis

Tangled web of interactions among proteins involved in iron–sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies

Contact Info

Product

Resources

About