Structure-based ligand binding sites of protein p14.5, a member of protein family YER057c/YIL051c/YjgF

Mistiniene, Edita; Pozdniakovaite, Natalija; Popendikyte, Violeta; Naktinis, Vytautas

doi:10.1016/j.ijbiomac.2005.08.008

Cited by 15 publications

(13 citation statements)

References 24 publications

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“…The C-terminal portion of Dph6 contains two domains related to the YjgF-YER057c-UK114 protein family (eu_AANH_C1: cd06155 and eu_AANH_C2: cd06166) that may promote homotrimerisation and formation of an inter-subunit cleft that has been proposed to bind small molecule ligands [63]–[65]. Several key residues in human UK114 required for homotrimerisation and ligand binding [66] are present in Dph6 (Figure S8) including arg-107, which in E. coli TdcF forms a bidentate salt bridge with the carboxylic acid group of bound ligands [63]. Deletion of residues 335–415 encompassing much of the YjgF-YER057c-UK114 region abolished the function of Dph6 as monitored by sordarin resistance (Figure 7), while truncation of Dph6 at the first of the two conserved domains by insertion of a myc tag also eliminated Dph6 function (Figure 7) despite detectable expression of the truncated polypeptide (data not shown), indicating that the YjgF-YER057c-UK114 domains are also important for Dph6 function and that the Alpha_ANH_like_IV domain is nonfunctional on its own.…”

Section: Discussionmentioning

confidence: 99%

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The Amidation Step of Diphthamide Biosynthesis in Yeast Requires DPH6, a Gene Identified through Mining the DPH1-DPH5 Interaction Network

et al. 2013

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Diphthamide is a highly modified histidine residue in eukaryal translation elongation factor 2 (eEF2) that is the target for irreversible ADP ribosylation by diphtheria toxin (DT). In Saccharomyces cerevisiae, the initial steps of diphthamide biosynthesis are well characterized and require the DPH1-DPH5 genes. However, the last pathway step—amidation of the intermediate diphthine to diphthamide—is ill-defined. Here we mine the genetic interaction landscapes of DPH1-DPH5 to identify a candidate gene for the elusive amidase (YLR143w/DPH6) and confirm involvement of a second gene (YBR246w/DPH7) in the amidation step. Like dph1-dph5, dph6 and dph7 mutants maintain eEF2 forms that evade inhibition by DT and sordarin, a diphthamide-dependent antifungal. Moreover, mass spectrometry shows that dph6 and dph7 mutants specifically accumulate diphthine-modified eEF2, demonstrating failure to complete the final amidation step. Consistent with an expected requirement for ATP in diphthine amidation, Dph6 contains an essential adenine nucleotide hydrolase domain and binds to eEF2. Dph6 is therefore a candidate for the elusive amidase, while Dph7 apparently couples diphthine synthase (Dph5) to diphthine amidation. The latter conclusion is based on our observation that dph7 mutants show drastically upregulated interaction between Dph5 and eEF2, indicating that their association is kept in check by Dph7. Physiologically, completion of diphthamide synthesis is required for optimal translational accuracy and cell growth, as indicated by shared traits among the dph mutants including increased ribosomal −1 frameshifting and altered responses to translation inhibitors. Through identification of Dph6 and Dph7 as components required for the amidation step of the diphthamide pathway, our work paves the way for a detailed mechanistic understanding of diphthamide formation.

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Section: Discussionmentioning

confidence: 99%

“…Note that the last two sequences appear twice in the alignment so that the sequence relationships to each of the YjgF-YER057c-UK114 related domains in the non-mammalian proteins can be shown. *, conserved residues shown to be important for trimerisation and ligand binding [63], [66].…”

Section: Supporting Informationmentioning

confidence: 99%

The Amidation Step of Diphthamide Biosynthesis in Yeast Requires DPH6, a Gene Identified through Mining the DPH1-DPH5 Interaction Network

et al. 2013

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“…and has endoribonuclease activity (Morishita et al 1999;Mistiniene et al 2003Mistiniene et al , 2005. Although it is unknown whether the trimeric structure of HRSP12 is critical for its endoribonucleolytic activity, it is possible that the trimerization of HRSP12 is involved in maintaining the structural integrity of a functionally active GMD complex.…”

Section: The Integrity Of the Gmd Complex Is Necessary For Gmdmentioning

confidence: 99%

“…To test the above possibility, we constructed two variants: λN-HA-HRSP12-R107E and λN-HA-HRSP12-P105A/R107E. Previous data showed that these variants fail to form a trimeric structure (Mistiniene et al 2005). The results of tethering experiments in which comparable expression of effectors was demonstrated by Western blotting (Supplemental Fig.…”

Section: The Integrity Of the Gmd Complex Is Necessary For Gmdmentioning

confidence: 99%

Identification and molecular characterization of cellular factors required for glucocorticoid receptor-mediated mRNA decay

Park

et al. 2016

Genes Dev.

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Glucocorticoid (GC) receptor (GR) has been shown recently to bind a subset of mRNAs and elicit rapid mRNA degradation. However, the molecular details of GR-mediated mRNA decay (GMD) remain unclear. Here, we demonstrate that GMD triggers rapid degradation of target mRNAs in a translation-independent and exon junction complexindependent manner, confirming that GMD is mechanistically distinct from nonsense-mediated mRNA decay (NMD). Efficient GMD requires PNRC2 (proline-rich nuclear receptor coregulatory protein 2) binding, helicase ability, and ATM-mediated phosphorylation of UPF1 (upstream frameshift 1). We also identify two GMD-specific factors: an RNA-binding protein, YBX1 (Y-box-binding protein 1), and an endoribonuclease, HRSP12 (heat-responsive protein 12). In particular, using HRSP12 variants, which are known to disrupt trimerization of HRSP12, we show that HRSP12 plays an essential role in the formation of a functionally active GMD complex. Moreover, we determine the hierarchical recruitment of GMD factors to target mRNAs. Finally, our genome-wide analysis shows that GMD targets a variety of transcripts, implicating roles in a wide range of cellular processes, including immune responses.

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“…Examination of the OrfB amino acid sequence reveals that it contains all of the eight residues implicated in ligand binding (Y18, G32, Q33, F86, N90, P102, R104, and E118) as determined from the crystal structures of E. coli and human YjgF/ YER057c/UK114 family proteins (32,55). Although C107 in TdcF (an E. coli family member) has also been identified as an important residue for 2-ketobutyrate binding, it is not as conserved as the other eight active site residues and is not found in either the human YjgF/YER057c/UK114 family protein nor OrfB (11,55).…”

Section: Discussionmentioning

confidence: 99%

Alanylclavam Biosynthetic Genes Are Clustered Together with One Group of Clavulanic Acid Biosynthetic Genes inStreptomyces clavuligerus

et al. 2008

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Streptomyces clavuligerus produces at least five different clavam metabolites, including clavulanic acid and the methionine antimetabolite, alanylclavam. In vitro transposon mutagenesis was used to analyze a 13-kb region upstream of the known paralogue gene cluster. The paralogue cluster includes one group of clavulanic acid biosynthetic genes in S. clavuligerus. Twelve open reading frames (ORFs) were found in this area, and mutants were generated in each using either in vitro transposon or PCR-targeted mutagenesis. Mutants with defects in any of the genes orfA, orfB, orfC, or orfD were unable to produce alanylclavam but could produce all of the other clavams, including clavulanic acid. orfA encodes a predicted hydroxymethyltransferase, orfB encodes a YjgF/ YER057c/UK114-family regulatory protein, orfC encodes an aminotransferase, and orfD encodes a dehydratase. All of these types of proteins are normally involved in amino acid metabolism. Mutants in orfC or orfD also accumulated a novel clavam metabolite instead of alanylclavam, and a complemented orfC mutant was able to produce trace amounts of alanylclavam while still producing the novel clavam. Mass spectrometric analyses, together with consideration of the enzymes involved in its production, led to tentative identification of the novel clavam as 8-OH-alanylclavam, an intermediate in the proposed alanylclavam biosynthetic pathway.

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Structure-based ligand binding sites of protein p14.5, a member of protein family YER057c/YIL051c/YjgF

Cited by 15 publications

References 24 publications

The Amidation Step of Diphthamide Biosynthesis in Yeast Requires DPH6, a Gene Identified through Mining the DPH1-DPH5 Interaction Network

The Amidation Step of Diphthamide Biosynthesis in Yeast Requires DPH6, a Gene Identified through Mining the DPH1-DPH5 Interaction Network

Identification and molecular characterization of cellular factors required for glucocorticoid receptor-mediated mRNA decay

Alanylclavam Biosynthetic Genes Are Clustered Together with One Group of Clavulanic Acid Biosynthetic Genes inStreptomyces clavuligerus

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