Crystal structure of YIGZ, a conserved hypothetical protein from <i>Escherichia coli k12</i> with a novel fold

Park, Frances; Gajiwala, K.S.; Eroshkina, Galina; Furlong, E.B.; He, Dengming; Batiyenko, Yelena; Romero, R.; Christopher, Jon A.; Badger, John; Hendle, J.; Lin, Johann; Peat, Thomas S.; Buchanan, Sean G.

doi:10.1002/prot.20087

Cited by 10 publications

(13 citation statements)

References 19 publications

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“…An example is DUF1949 (IPR015269), a domain that is only found in the three analyzed Phytophthora species. This domain is observed in functional uncharacterized bacterial proteins like YIGZ in Escherichia coli K12 and adopts a ferredoxin-like fold (Park et al, 2004). The Phytophthora and bacterial proteins containing DUF1949 also contain a second, N-terminal uncharacterized protein family, UPF (UPF00029, IPR001498).…”

Section: Clustering Of Abundance Profiles Reveals Additional Potentiamentioning

confidence: 99%

A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization

et al. 2010

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Oomycetes comprise a diverse group of organisms that morphologically resemble fungi but belong to the stramenopile lineage within the supergroup of chromalveolates. Recent studies have shown that plant pathogenic oomycetes have expanded gene families that are possibly linked to their pathogenic lifestyle. We analyzed the protein domain organization of 67 eukaryotic species including four oomycete and five fungal plant pathogens. We detected 246 expanded domains in fungal and oomycete plant pathogens. The analysis of genes differentially expressed during infection revealed a significant enrichment of genes encoding expanded domains as well as signal peptides linking a substantial part of these genes to pathogenicity. Overrepresentation and clustering of domain abundance profiles revealed domains that might have important roles in hostpathogen interactions but, as yet, have not been linked to pathogenicity. The number of distinct domain combinations (bigrams) in oomycetes was significantly higher than in fungi. We identified 773 oomycete-specific bigrams, with the majority composed of domains common to eukaryotes. The analyses enabled us to link domain content to biological processes such as host-pathogen interaction, nutrient uptake, or suppression and elicitation of plant immune responses. Taken together, this study represents a comprehensive overview of the domain repertoire of fungal and oomycete plant pathogens and points to novel features like domain expansion and species-specific bigram types that could, at least partially, explain why oomycetes are such remarkable plant pathogens.

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Section: Clustering Of Abundance Profiles Reveals Additional Potentiamentioning

confidence: 99%

A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization

et al. 2010

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“…The analysis was made through visualization of the superimposed structures using PyMOL (53) and various alignments produced with CLUSTAL. COOT (31) was used for the superposition (32) of the atomic coordinates of the models and Protein Data Bank files as follows: 1UKX (14) and 1VI7 (25). DALI (33), SCOP (34), CATH (35), and PFAM (36) were also used.…”

Section: Methodsmentioning

confidence: 99%

“…Because of the larger than expected size, we next proceeded to determine whether the peak eluting at 48 kDa could represent a dimer. Although structural data suggest that neither the Gcn2 RWD domain nor YigZ form dimers (14,25), the presence of the charged linker region could be mediating electrostatic intermolecular interactions. We therefore performed size exclusion chromatography in the presence of the chaotropic agent potassium iodide.…”

Section: Structure-based Sequence Comparison and Modeling Of Yih1mentioning

confidence: 95%

“…6B). The structural features of the UPF0029 domain of YigZ (Protein Data Bank code 1VI7), determined by crystallography (25), are indicated at the bottom of the alignment. This alignment also includes sequences in the Yih1 family of proteins that separate this domain from the RWD domain and that are not found in the prokaryotic family.…”

Section: Structure-based Sequence Comparison and Modeling Of Yih1mentioning

confidence: 99%

“…7B) (25). 1Vl7 has a unique fold and consists of an ␣-␤ three-layer sandwich of one ␣-helix on one side, a five-stranded ␤-sheet in the middle, and two ␣-helices on the other side (Fig.…”

Section: Structure-based Sequence Comparison and Modeling Of Yih1mentioning

confidence: 99%

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Gcn1 and Actin Binding to Yih1

Sattlegger

Barbosa

Moraes

et al. 2011

Journal of Biological Chemistry

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Yeast Yih1 protein and its mammalian ortholog IMPACT, abundant in neurons, are inhibitors of Gcn2, a kinase involved in amino acid homeostasis, stress response, and memory formation. Like Gcn2, Yih1/IMPACT harbors an N-terminal RWD domain that mediates binding to the Gcn2 activator Gcn1. Yih1 competes with Gcn2 for Gcn1 binding, thus inhibiting Gcn2. Yih1 also binds G-actin. Here, we show that Yih1-actin interaction is independent of Gcn1 and that Yih1-Gcn1 binding does not require actin. The Yih1 RWD (residues 1-132) was sufficient for Gcn2 inhibition and Gcn1 binding, but not for actin binding, showing that actin binding is dispensable for inhibiting Gcn2. Actin binding required Yih1 residues 68 -258, encompassing part of the RWD and the C-terminal "ancient domain"; however, residues Asp-102 and Glu-106 in helix3 of the RWD were essential for Gcn1 binding and Gcn2 inhibition but dispensable for actin binding. Thus, the Gcn1-and actin-binding sites overlap in the RWD but have distinct binding determinants. Unexpectedly, Yih1 segment 68 -258 was defective for inhibiting Gcn2 even though it binds Gcn1 at higher levels than does full-length Yih1. This and other results suggest that Yih1 binds with different requirements to distinct populations of Gcn1 molecules, and its ability to disrupt Gcn1-Gcn2 complexes is dependent on a complete RWD and hindered by actin binding. Modeling of the ancient domain on the bacterial protein YigZ showed peculiarities to the eukaryotic and prokaryotic lineages, suggesting binding sites for conserved cellular components. Our results support a role for Yih1 in a cross-talk between the cytoskeleton and translation.In all eukaryotes, phosphorylation of the ␣-subunit of translation initiation factor 2 (eIF2␣) 5 is a major mechanism for the regulation of protein synthesis in response to a variety of environmental or intracellular stresses. This event leads to general translation inhibition at the same time that it allows for increased translation of specific messages, such as GCN4 in yeast and ATF4 in mammals. These code for transcription factors that activate a network of genes aimed at cell recovery from the initial stress (1).Gcn2, the sole eIF2␣ kinase in the yeast Saccharomyces cerevisiae, is activated by amino acid starvation and imbalance and other stresses (2). Gcn2 is a highly conserved protein found in all eukaryotic organisms, and in mammals it has been implicated in additional functions such as modulating the immune system, feeding behavior, and memory formation (3-6). Gcn2 is composed of five distinct functional domains. At its N terminus, a region called the RWD domain (from its presence in RING finger proteins, WD-repeat-containing proteins, and yeast DEAD-like helicases) (7) binds directly to the activator protein Gcn1 (8, 9). Its kinase catalytic domain is found in the center of the protein. Between the RWD domain and the kinase domain resides a pseudo-kinase domain, identifiable by characteristic but incomplete protein kinase sequences, with no well defined function. A d...

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Experimentally based structural model of Yih1 provides insight into its function in controlling the key translational regulator Gcn2

Harjes

Jameson

et al. 2020

FEBS Letters

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Yeast impact homolog 1 (Yih1), or IMPACT in mammals, is part of a conserved regulatory module controlling the activity of General Control Nonderepressible 2 (Gcn2), a protein kinase that regulates protein synthesis. Yih1/IMPACT is implicated not only in many essential cellular processes, such as neuronal development, immune system regulation and the cell cycle, but also in cancer. Gcn2 must bind to Gcn1 in order to impair the initiation of protein translation. Yih1 hinders this key Gcn1‐Gcn2 interaction by binding to Gcn1, thus preventing Gcn2‐mediated inhibition of protein synthesis. Here, we solved the structures of the two domains of Saccharomyces cerevisiae Yih1 separately using Nuclear Magnetic Resonance and determined the relative positions of the two domains using a range of biophysical methods. Our findings support a compact structural model of Yih1 in which the residues required for Gcn1 binding are buried in the interface. This model strongly implies that Yih1 undergoes a large conformational rearrangement from a latent closed state to a primed open state to bind Gcn1. Our study provides structural insight into the interactions of Yih1 with partner molecules.

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Crystal structure of YIGZ, a conserved hypothetical protein from Escherichia coli k12 with a novel fold

Cited by 10 publications

References 19 publications

A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization

A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization

Gcn1 and Actin Binding to Yih1

Experimentally based structural model of Yih1 provides insight into its function in controlling the key translational regulator Gcn2

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