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1.
Biochem Biophys Res Commun ; 699: 149499, 2024 Mar 05.
Article in English | MEDLINE | ID: mdl-38281328

ABSTRACT

In yeast, ras-like small G proteins, Gtr1p and Gtr2p, form heterodimers that affect cell division, detect amino acids, and regulate the activity of TORC1, a protein complex that integrates various signals, including those related to nutrient availability, growth factors, and stress signals. To explore novel roles of Gtr2p, yeast two-hybrid screening was performed using gtr2S23Np, an active form of Gtr2p, which identified Rps31p and Rpl12p as Gtr2p-interacting proteins. In the present study, we found that Gtr2p, but not Gtr1p, interacts with Rps31p, a 40S ribosomal subunit, and a component of the ubiquitin fusion protein Ubi3p, which is essential for the initiation and elongation of translation. In yeast cells expressing gtr2Q66Lp, an inactive form of Gtr2p, the interaction between Rps31p and gtr2Q66Lp, as well as the level of exogenous expression of Rps31p, was reduced. However, the level of exogenous expression of Rpl12p was unaffected. Introducing a mutation in ubiquitin target lysine residues to arginine (rps31-K5R) restored the level of exogenously expressed Rps31p and rescued the rapamycin and caffeine sensitivity of gtr2Q66L cells. Sucrose density gradient centrifugation of yeast cell lysate expressing Rps31p and gtr2Q66Lp revealed that exogenously expressed Rps31p was poorly incorporated, whereas rps31-K5Rp was efficiently incorporated, into ribosomes. These results suggest that Gtr2p influences incorporation of Rps31p into ribosomes and contributes to drug resistance through its interaction with Rps31p.


Subject(s)
Monomeric GTP-Binding Proteins , Saccharomyces cerevisiae Proteins , Monomeric GTP-Binding Proteins/metabolism , Ribosomal Proteins/genetics , Ribosomal Proteins/metabolism , Ribosomes/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Ubiquitins/metabolism
2.
Biochem Biophys Res Commun ; 598: 107-112, 2022 04 02.
Article in English | MEDLINE | ID: mdl-35158208

ABSTRACT

Yeast Gtr1p is a GTPase that forms a heterodimer with Gtr2p, another GTPase; it is involved in regulating TORC1 activity in nutrient signaling, including amino acid availability and growth control. Gtr1p is a positive regulator of TORC1, a kinase that regulates various cellular functions (e.g., protein synthesis and autophagy) under specific nutrient and environmental conditions, including oxidative stress. In this study, we examined the roles of Gtr1p in oxidative stress responses. We found that yeast cells expressing guanosine diphosphatase (GDP)-bound Gtr1p (Gtr1-S20Lp) were resistant to hydrogen peroxide (H2O2), whereas guanosine triphosphate (GTP)-bound Gtr1p (Gtr1-Q65Lp) was sensitive to H2O2 compared with the wild type. Consistent with these findings, yeast cells lacking Iml1p, a component of the GTPase-activating protein complex for Gtr1p, exhibited the H2O2-sensitive phenotype. In gtr1S20L cells, autophagy was highly induced under oxidative stress. gtr1Q65L cells showed decreased expression of the SNQ2 gene, which encodes a multidrug transporter involved in resistance to oxidative stress, and the overexpression of SNQ2 rescued the oxidative stress sensitivity of gtr1Q65L cells. These results suggest that Gtr1p is involved in oxidative stress responses through mechanisms that include autophagy and SNQ2 expression.


Subject(s)
Monomeric GTP-Binding Proteins/metabolism , Oxidative Stress/physiology , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/physiology , ATP-Binding Cassette Transporters/genetics , ATP-Binding Cassette Transporters/metabolism , Autophagy , Gene Expression Regulation, Fungal , Hydrogen Peroxide/pharmacology , Monomeric GTP-Binding Proteins/genetics , Oxidative Stress/drug effects , Saccharomyces cerevisiae/drug effects , Saccharomyces cerevisiae Proteins/genetics
3.
Biochem Biophys Res Commun ; 547: 169-175, 2021 04 02.
Article in English | MEDLINE | ID: mdl-33610917

ABSTRACT

WDR35/IFT121 is an intraflagellar transport protein in primary cilia, which is associated with RagA, an mTORC1-activating protein. To elucidate the functions of the interaction between WDR35 and RagA in primary cilia, as well as mTOR signaling, we identified WDR35-interacting proteins using mass spectrometry. We found that WDR35 associates with CCT complex proteins including TCP1/CCT1, which act as molecular chaperones for α-tubulin folding. Immunostaining showed that acetylated α-tubulin was concentrated in the vicinity of primary cilia in 293T cells. In contrast, acetylated tubulin was dispersed in WDR35 partial knockout cells established from 293T cells. Similarly, scattered subcellular localization of acetylated tubulin was observed in RagA knockout cells. RagA was present in the primary cilia of NIH3T3 cells, and the GDP form of RagA exhibited strong binding to WDR35 and negative regulation of primary cilium formation. These results suggest that WDR35 is involved in the subcellular localization of acetylated tubulin in primary cilia via its interactions with TCP1 and/or RagA family proteins.


Subject(s)
Cilia/metabolism , Cytoskeletal Proteins/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Tubulin/metabolism , Acetylation , Animals , Cells, Cultured , HEK293 Cells , Humans , Mechanistic Target of Rapamycin Complex 1/metabolism , Mice , Monomeric GTP-Binding Proteins/metabolism , Signal Transduction , Subcellular Fractions/metabolism , Tubulin/chemistry
4.
Genes Cells ; 24(2): 151-161, 2019 Feb.
Article in English | MEDLINE | ID: mdl-30570184

ABSTRACT

Small Ras-like GTPases act as molecular switches for various signal transduction pathways. RagA, RagB/RagC and RagD are small Ras-like GTPases that play regulatory roles in mTORC1. Lack of proper activation of mTORC1 can lead to diseases, such as cancer and diabetes. In this study, we found an interaction between RagA and WDR35. Mutations of WDR35 may cause genetic diseases including Sensenbrenner syndrome. WDR35 seems to be a hedgehog signaling protein with a possible ciliary function and a possible upstream regulator of RagA. RagB is a homologue of RagA and is also associated with WDR35. WDR35 is present in the endoplasmic reticulum, but usually not in lysosomes, where Rag family proteins act as an mTORC1 switch. Over-expression of WDR35 results in decreased phosphorylation of ribosome S6 protein in a RagA-, RagB- and RagC-dependent manner. Thus, WDR35 is associated with RagA, RagB and RagC and might negatively influence mTORC1 activity.


Subject(s)
Mechanistic Target of Rapamycin Complex 1/metabolism , Monomeric GTP-Binding Proteins/metabolism , Multiprotein Complexes/metabolism , Proteins/metabolism , Cytoskeletal Proteins , HEK293 Cells , Hedgehog Proteins , Humans , Intracellular Signaling Peptides and Proteins , Lysosomes/metabolism , Mechanistic Target of Rapamycin Complex 1/genetics , Monomeric GTP-Binding Proteins/genetics , Multiprotein Complexes/genetics , Phosphorylation , Protein Binding , Protein Interaction Domains and Motifs , Proteins/genetics , Signal Transduction , Two-Hybrid System Techniques
5.
Proc Natl Acad Sci U S A ; 115(26): 6715-6720, 2018 06 26.
Article in English | MEDLINE | ID: mdl-29891675

ABSTRACT

In aerobically growing cells, the guanine base of RNA is oxidized to 8-oxo-7,8-dihydroguanine (8-oxoG), which induces alteration in their gene expression. We previously demonstrated that the human AUF1 protein binds to 8-oxoG in RNA to induce the selective degradation of oxidized messenger RNA. We herein report that the poly(C)-binding protein PCBP1 binds to more severely oxidized RNA to activate apoptosis-related reactions. While AUF1 binds to oligoribonucleotides carrying a single 8-oxoG, PCBP1 does not bind to such oligoribonucleotides but instead binds firmly to oligoribonucleotides in which two 8-oxoG residues are located nearby. PCBP1-deficient cells, constructed from the human HeLa S3 line using the CRISPR-Cas9 system, exhibited higher survival rates than HeLa S3 cells when small doses of hydrogen peroxide were applied. The levels of caspase-3 activation and PARP-1 cleavage in the PCBP1-deficient cells were significantly lower than those in wild-type cells. The structure-function relationship of PCBP1 was established with the use of PCBP1 mutant proteins in which the conserved KH domains were defective. Human cells appear to possess two distinct mechanisms, one controlled by AUF1 and the other by PCBP1, with the former functioning when messenger RNA is moderately oxidized and the latter operating when the RNA is more severely damaged.


Subject(s)
Apoptosis/physiology , Heterogeneous-Nuclear Ribonucleoproteins/metabolism , RNA, Messenger/metabolism , Amino Acid Substitution , CRISPR-Cas Systems , Caspase 3/physiology , Conserved Sequence , DNA-Binding Proteins , Guanine/analogs & derivatives , Guanine/metabolism , HeLa Cells , Heterogeneous Nuclear Ribonucleoprotein D0 , Heterogeneous-Nuclear Ribonucleoprotein D/metabolism , Heterogeneous-Nuclear Ribonucleoproteins/chemistry , Humans , Hydrogen Peroxide/pharmacology , Oxidation-Reduction , Protein Domains , RNA, Messenger/chemistry , RNA-Binding Proteins , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Structure-Activity Relationship
6.
Free Radic Biol Med ; 79: 109-16, 2015 Feb.
Article in English | MEDLINE | ID: mdl-25486179

ABSTRACT

In aerobically growing cells, in which reactive oxygen species are produced, the guanine base of RNA is oxidized to 8-oxo-7,8-dihydroguanine, which induces alterations in gene expression. Here we show that the human Auf1 protein, also called HNRNPD, binds specifically to RNA containing this oxidized base and may be involved in cellular processes associated with managing the problems caused by RNA oxidation. Auf1-deficient cells were constructed from human HeLa and Nalm-6 lines using two different targeting procedures. Both types of Auf1-deficient cells are viable, but exhibit growth retardation. The stability of messenger RNA for four different housekeeping genes was determined in Auf1-deficient and -proficient cells, treated with or without hydrogen peroxide. The level of oxidized messenger RNA was considerably higher in Auf1-deficient cells than in Auf1-proficient cells. Auf1 may play a role in the elimination of oxidized RNA, which is required for the maintenance of proper gene expression under conditions of oxidative stress.


Subject(s)
Heterogeneous-Nuclear Ribonucleoprotein D/physiology , Oxidative Stress , RNA, Messenger/metabolism , Cell Line , Heterogeneous Nuclear Ribonucleoprotein D0 , Humans
7.
Genes Cells ; 19(6): 449-63, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24702707

ABSTRACT

The yeast Ras-like GTPases Gtr1p and Gtr2p form a heterodimer, are implicated in the regulation of TOR complex 1 (TORC1) and play pivotal roles in cell growth. Gtr1p and Gtr2p bind Ego1p and Ego3p, which are tethered to the endosomal and vacuolar membranes where TORC1 functions are regulated through a relay of amino acid signaling interactions. The mechanisms by which Gtr1p and Gtr2p activate TORC1 remain obscure. We probed the interactions of the Gtr1p-Gtr2p complex with the Ego1p-Ego3p complex and TORC1 subunits. Mutations in the region (179-220 a.a.) following the nucleotide-binding region of Gtr1p and Gtr2p abrogated their mutual interaction and resulted in a loss in function, suggesting that complex formation between Gtr1p and Gtr2p was indispensable for TORC1 function. A modified yeast two-hybrid assay showed that Gtr1p-Gtr2p complex formation is important for its interaction with the Ego1p-Ego3p complex. GTP-bound Gtr1p interacted with the region containing the HEAT repeats of Kog1p and the C-terminal region of Tco89p. The GTP-bound Gtr2p suppressed a Kog1p mutation. Our findings indicate that the interactions of the Gtr1p-Gtr2p complex with the Ego1p-Ego3p complex and TORC1 components Kog1p and Tco89p play a role in TORC1 function.


Subject(s)
Amino Acids/metabolism , Membrane Proteins/metabolism , Monomeric GTP-Binding Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Transcription Factors/metabolism , Monomeric GTP-Binding Proteins/genetics , Mutation , Protein Multimerization , Saccharomyces cerevisiae Proteins/genetics
8.
Cells ; 3(2): 180-98, 2014 Mar 27.
Article in English | MEDLINE | ID: mdl-24709957

ABSTRACT

The yeast ubiquitin-like and ubiquitin-associated protein Dsk2 is one of the ubiquitin receptors that function in the ubiquitin-proteasome pathway. We screened the Dsk2-interacting proteins in Saccharomyces cerevisiae by a two-hybrid assay and identified a novel Dsk2-interacting protein, Irc22, the gene locus of which has previously been described as YEL001C, but the function of which is unknown. IRC22/YEL001C encodes 225 amino acid residues with a calculated molecular weight of 25 kDa. The Irc22 protein was detected in yeast cells. IRC22 was a nonessential gene for yeast growth, and its homologs were found among ascomycetous yeasts. Irc22 interacted with Dsk2 in yeast cells, but not with Rad23 and Ddi1. Ubiquitin-dependent degradation was impaired mildly by over-expression or disruption of IRC22. Compared with the wild-type strain, dsk2D exhibited salt sensitivity while irc22D exhibited salt tolerance at high temperatures. The salt-tolerant phenotype that was observed in irc22D disappeared in the dsk2Dirc22D double disruptant, indicating that DSK2 is positively and IRC22 is negatively involved in salt stress tolerance. IRC22 disruption did not affect any responses to DNA damage and oxidative stress when comparing the irc22D and wild-type strains. Collectively, these results suggest that Dsk2 and Irc22 are involved in salt stress tolerance in yeast.

9.
J Biol Chem ; 288(46): 32952-62, 2013 Nov 15.
Article in English | MEDLINE | ID: mdl-24097971

ABSTRACT

In aerobically growing cells, in which reactive oxygen species are produced, the guanine base is oxidized to 8-oxo-7,8-dihydroguanine, which can pair with adenine as well as cytosine. This mispairing causes alterations in gene expression, and cells possess mechanisms to prevent such outcomes. In Escherichia coli, 8-oxo-7,8-dihydroguanine-related phenotypic suppression of lacZ amber is enhanced by mutations in genes related to the prevention of abnormal protein synthesis under oxidative stress. A genome-wide search for the genes responsible, followed by DNA sequence determination, revealed that specific amino acid changes in guanylate kinase and in the ß and ß' subunits of RNA polymerase cause elevated levels of phenotypic suppression, specifically under aerobic conditions. The involvement of the DnaB, DnaN, and MsbA proteins, which are involved in DNA replication and in preserving the membrane structure, was also noted. Interactions of these proteins with each other and also with other molecules may be important for preventing errors in gene expression.


Subject(s)
DNA-Directed RNA Polymerases/metabolism , Escherichia coli K12/enzymology , Escherichia coli Proteins/metabolism , Guanylate Kinases/metabolism , Oxidative Stress/physiology , ATP-Binding Cassette Transporters/genetics , ATP-Binding Cassette Transporters/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , DNA Polymerase III/genetics , DNA Polymerase III/metabolism , DNA-Directed RNA Polymerases/genetics , DnaB Helicases/genetics , DnaB Helicases/metabolism , Escherichia coli K12/genetics , Escherichia coli Proteins/genetics , Genome-Wide Association Study , Guanine/analogs & derivatives , Guanine/metabolism , Guanylate Kinases/genetics , Oxidation-Reduction
10.
J Biol Chem ; 288(12): 8128-8135, 2013 Mar 22.
Article in English | MEDLINE | ID: mdl-23376345

ABSTRACT

Reactive oxygen species are produced as side products of oxygen utilization and can lead to the oxidation of nucleic acids and their precursor nucleotides. Among the various oxidized bases, 8-oxo-7,8-dihydroguanine seems to be the most critical during the transfer of genetic information because it can pair with both cytosine and adenine. During the de novo synthesis of guanine nucleotides, GMP is formed first, and it is converted to GDP by guanylate kinase. This enzyme hardly acts on an oxidized form of GMP (8-oxo-GMP) formed by the oxidation of GMP or by the cleavage of 8-oxo-GDP and 8-oxo-GTP by MutT protein. Although the formation of 8-oxo-GDP from 8-oxo-GMP is thus prevented, 8-oxo-GDP itself may be produced by the oxidation of GDP by reactive oxygen species. The 8-oxo-GDP thus formed can be converted to 8-oxo-GTP because nucleoside-diphosphate kinase and adenylate kinase, both of which catalyze the conversion of GDP to GTP, do not discriminate 8-oxo-GDP from normal GDP. The 8-oxo-GTP produced in this way and by the oxidation of GTP can be used for RNA synthesis. This misincorporation is prevented by MutT protein, which has the potential to cleave 8-oxo-GTP as well as 8-oxo-GDP to 8-oxo-GMP. When (14)C-labeled 8-oxo-GTP was applied to CaCl2-permeabilized cells of a mutT(-) mutant strain, it could be incorporated into RNA at 4% of the rate for GTP. Escherichia coli cells appear to possess mechanisms to prevent misincorporation of 8-oxo-7,8-dihydroguanine into RNA.


Subject(s)
Deoxyguanine Nucleotides/metabolism , Escherichia coli/enzymology , RNA, Bacterial/biosynthesis , Adenosine Triphosphate/chemistry , Adenylate Kinase/chemistry , Cytidine Triphosphate/chemistry , Deoxyguanine Nucleotides/chemistry , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Guanosine Monophosphate/chemistry , Guanylate Kinases/chemistry , Kinetics , Nucleoside-Diphosphate Kinase/chemistry , Oxidation-Reduction , Pyrophosphatases/chemistry , RNA, Bacterial/metabolism , Uridine Triphosphate/chemistry
11.
Acta Crystallogr D Biol Crystallogr ; 67(Pt 10): 894-901, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21931221

ABSTRACT

Chlamydomonas reinhardtii α-type carbonic anhydrase (Cr-αCA1) is a dimeric enzyme that catalyses the interconversion of carbon dioxide and carbonic acid. The precursor form of Cr-αCA1 undergoes post-translational cleavage and N-glycosylation. Comparison of the genomic sequences of precursor Cr-αCA1 and other αCAs shows that Cr-αCA1 contains a different N-terminal sequence and two insertion sequences. A 35-residue peptide in one of the insertion sequences is deleted from the precursor during maturation. The crystal structure of the mature form of Cr-αCA1 has been determined at 1.88 Šresolution. Each subunit is cleaved into the long and short peptides, but they are linked together by a disulfide bond. The two subunits are linked by a disulfide bond. N-Glycosylations occur at three asparagine residues and the attached N-glycans protrude into solvent regions. The subunits consist of a core ß-sheet structure composed of nine ß-strands. At the centre of the ß-sheet is the catalytic site, which contains a Zn atom bound to three histidine residues. The amino-acid residues around the Zn atom are highly conserved in other monomeric and dimeric αCAs. The short peptide runs near the active site and forms a hydrogen bond to the zinc-coordinated residue in the long chain, suggesting an important role for the short peptide in Cr-αCA1 activity.


Subject(s)
Carbonic Anhydrases/chemistry , Carbonic Anhydrases/metabolism , Chlamydomonas reinhardtii/enzymology , Amino Acid Sequence , Asparagine/metabolism , Carbonic Anhydrases/genetics , Catalytic Domain , Conserved Sequence , Crystallography, X-Ray , Dimerization , Disulfides/chemistry , Glycosylation , Models, Molecular , Molecular Sequence Data , Protein Conformation , Zinc/metabolism
12.
Biochem Biophys Res Commun ; 411(3): 555-61, 2011 Aug 05.
Article in English | MEDLINE | ID: mdl-21763274

ABSTRACT

Ubiquitin-like (UBL)-ubiquitin-associated (UBA) proteins, including Dsk2 and Rad23, act as delivery factors that target polyubiquitinated substrates to the proteasome. We report here that the Dsk2 UBL domain is ubiquitinated in yeast cells and that Dsk2 ubiquitination of the UBL domain is involved in Dsk2 stability, depending on the Dsk2 UBA domain. Also, Dsk2 lacking ubiquitin chains impaired ubiquitin-dependent protein degradation and decreased the interaction of Dsk2 with polyubiquitinated proteins in cells. Moreover, Dsk2 ubiquitination affected ability to restore the temperature-sensitive growth defect of dsk2Δ. These results indicate that ubiquitination in the UBL domain of Dsk2 has in vivo functions in the ubiquitin-proteasome pathway in yeast.


Subject(s)
Cell Cycle Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Ubiquitin/metabolism , Ubiquitination , Ubiquitins/metabolism , Amino Acid Sequence , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/genetics , Molecular Sequence Data , Protein Stability , Protein Structure, Tertiary , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Ubiquitins/chemistry , Ubiquitins/genetics
13.
J Antibiot (Tokyo) ; 63(11): 661-5, 2010 Nov.
Article in English | MEDLINE | ID: mdl-20842142

ABSTRACT

Actinohivin (AH) is a microbial lectin containing 114 amino acids, which inhibits human immunodeficiency virus (HIV) infection. This effect is brought about by its specific binding to Man-α(1-2)-Man unit(s) of high-mannose type glycan (HMTG) bound to HIV gp120. The recently determined crystal structure of AH suggests that three repeated segments (the residue numbers 1-38, 39-76 and 77-114 for segments 1, 2 and 3, respectively) form three sugar-binding pockets to accommodate Man-α(1-2)-Man units. The strong specific binding of AH to gp120 is considered to be due to multivalent interaction of the three sugar-binding pockets with three HMTGs of gp120 via the 'cluster effect' of lectin. It remains to be seen which residues of the sugar-binding pockets are essential for acceptance of Man-α(1-2)-Man. To identify the amino acid residues critical for anti-HIV effect, we performed mutational analysis. Mutant AHs were subjected to enzyme-linked immunosorbent assay testing for gp120-binding activity and to syncytium formation assay. As a result, it was revealed that Asp15, Tyr23, Leu25, Asn28 and Tyr32 in segment 1, Tyr61 in segment 2 and Tyr99 in segment 3 are essential for anti-HIV activity. The conserved residues, Asp53, Leu63, Asn66 and Tyr70, in segment 2 and, Asp91, Leu101, Asn104 and Tyr108, in segment 3 are also necessary. Furthermore, aromatic residues at positions 23 and 32 are required for creation of potency. These data will be useful for predicting the detailed mechanism of AH-Man-α(1-2)-Man/HMTG/gp120 interaction by computational analysis and for possible development of more potent microbicides for prevention of HIV transmission.


Subject(s)
Anti-HIV Agents/pharmacology , Bacterial Proteins/pharmacology , HIV Envelope Protein gp120/metabolism , HIV/drug effects , Amino Acid Sequence , Amino Acid Substitution , Anti-HIV Agents/chemistry , Anti-HIV Agents/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Binding Sites , Enzyme-Linked Immunosorbent Assay , HIV Infections/drug therapy , HIV Infections/virology , Humans , Mannose/metabolism , Mutation , Protein Binding
14.
Article in English | MEDLINE | ID: mdl-20823532

ABSTRACT

Carbonic anhydrases (CAs) are ubiquitously distributed and are grouped into three structurally independent classes (alphaCA, betaCA and gammaCA). Most alphaCA enzymes are monomeric, but alphaCA1 from Chlamydomonas reinhardtii is a dimer that is uniquely stabilized by disulfide bonds. In addition, during maturation an internal peptide of 35 residues is removed and three asparagine residues are glycosylated. In order to obtain insight into the effects of these structural features on CA function, wild-type C. reinhardtii alphaCA1 has been crystallized in space group P6(5), with unit-cell parameters a=b=134.3, c=120.2 A. The crystal diffracted to 1.88 A resolution and a preliminary solution of its crystal structure has been obtained by the MAD method.


Subject(s)
Carbonic Anhydrases/chemistry , Chlamydomonas reinhardtii/enzymology , Crystallography, X-Ray
15.
Chem Pharm Bull (Tokyo) ; 57(12): 1385-90, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19952449

ABSTRACT

The alkaline treatment and dehydrogenation of pyridinium salts, formed from the S-alkylations of 3-(1-pyridinio)thiophene-2-thiolates with alpha,alpha-dibromo-o-, m-, or p-xylene, provided the corresponding alpha,alpha'-bis[(thieno[3,4-b]indolizin-3-yl)thio]-o-, m-, and p-xylene derivatives in low to good yields. Both (1)H-NMR and UV-Vis spectra of these products supported distinctly the predominance of the gauche-gauche conformation in relation to the two sulfide linkages as the spacer in these molecules. On the other hand, the X-ray analyses indicated the expected gauche-gauche conformation for the m- and the p-xylene derivatives, but the anti-anti one for the o-xylene derivative.


Subject(s)
Heterocyclic Compounds/chemistry , Heterocyclic Compounds/chemical synthesis , Indolizines/chemistry , Indolizines/chemical synthesis , Nitrogen , Sulfhydryl Compounds/chemistry , Sulfhydryl Compounds/chemical synthesis , Xylenes/chemistry , Xylenes/chemical synthesis , Crystallography, X-Ray , Magnetic Resonance Spectroscopy , Molecular Conformation , Molecular Structure , Nitrogen/chemistry
16.
J Mol Biol ; 394(2): 286-96, 2009 Nov 27.
Article in English | MEDLINE | ID: mdl-19761773

ABSTRACT

In protein synthesis, threonyl-tRNA synthetase (ThrRS) must recognize threonine (Thr) from the 20 kinds of amino acids and the cognate tRNA(Thr) from different tRNAs in order to generate Thr-tRNA(Thr). In general, an organism possesses one kind of gene corresponding to ThrRS. However, it has been recently found that some organisms have two different genes for ThrRS in the genome, suggesting that their proteins ThrRS-1 and ThrRS-2 function separately and complement each other in the threonylation of tRNA(Thr), one for catalysis and the other for trans-editing of misacylated Ser-tRNA(Thr). In order to clarify their three-dimensional structures, we performed X-ray analyses of two putatively assigned ThrRSs from Aeropyrum pernix (ApThrRS-1 and ApThrRS-2). These proteins were overexpressed in Escherichia coli, purified, and crystallized. The crystal structure of ApThrRS-1 has been successfully determined at 2.3 A resolution. ApThrRS-1 is a dimeric enzyme composed of two identical subunits, each containing two domains for the catalytic reaction and for anticodon binding. The essential editing domain is completely missing as expected. These structural features reveal that ThrRS-1 catalyzes only the aminoacylation of the cognate tRNA, suggesting the necessity of the second enzyme ThrRS-2 for trans-editing. Since the N-terminal sequence of ApThrRS-2 is similar to the sequence of the editing domain of ThrRS from Pyrococcus abyssi, ApThrRS-2 has been expected to catalyze deaminoacylation of a misacylated serine moiety at the CCA terminus.


Subject(s)
Aeropyrum/metabolism , RNA, Archaeal/metabolism , RNA, Transfer, Amino Acyl/metabolism , Threonine-tRNA Ligase/chemistry , Transfer RNA Aminoacylation , Aeropyrum/enzymology , Amino Acid Sequence , Crystallography, X-Ray , Molecular Sequence Data , Protein Folding , Protein Structure, Tertiary , Threonine/metabolism , Threonine-tRNA Ligase/genetics , Threonine-tRNA Ligase/metabolism
17.
Proc Natl Acad Sci U S A ; 106(37): 15633-8, 2009 Sep 15.
Article in English | MEDLINE | ID: mdl-19717426

ABSTRACT

Various lectins have attracted attention as potential microbicides to prevent HIV transmission. Their capacity to bind glycoproteins has been suggested as a means to block HIV binding and entry into susceptible cells. The previously undescribed lectin actinohivin (AH), isolated by us from an actinomycete, exhibits potent in vitro anti-HIV activity by binding to high-mannose (Man) type glycans (HMTGs) of gp120, an envelope glycoprotein of HIV. AH contains 114 aa and consists of three segments, all of which need to show high affinity to gp120 for the anti-HIV characteristic. To generate the needed mechanistic understanding of AH binding to HIV in anticipation of seeking approval for human testing as a microbicide, we have used multiple molecular tools to characterize it. AH showed a weak affinity to Man alpha(1-2)Man, Man alpha(1-2)Man alpha(1-2)Man, of HMTG (Man8 or Man9) or RNase B (which has a single HMTG), but exhibited a strong and highly specific affinity (K(d) = 3.4 x 10(-8) M) to gp120 of HIV, which contains multiple Man8 and/or Man9 units. We have compared AH to an alternative lectin, cyanovirin-N, which did not display similar levels of discrimination between high- and low-density HMTGs. X-ray crystal analysis of AH revealed a 3D structure containing three sugar-binding pockets. Thus, the strong specific affinity of AH to gp120 is considered to be due to multivalent interaction of the three sugar-binding pockets with three HMTGs of gp120 via the "cluster effect" of lectin. Thus, AH is a good candidate for investigation as a safe microbicide to help prevent HIV transmission.


Subject(s)
Bacterial Proteins/pharmacology , HIV Fusion Inhibitors/pharmacology , HIV Infections/prevention & control , HIV-1/drug effects , Lectins/pharmacology , Bacterial Proteins/chemistry , Bacterial Proteins/pharmacokinetics , Binding Sites , Carrier Proteins/pharmacokinetics , Carrier Proteins/pharmacology , Crystallography, X-Ray , HIV Envelope Protein gp120/chemistry , HIV Fusion Inhibitors/chemistry , HIV Fusion Inhibitors/pharmacokinetics , HIV-1/pathogenicity , HIV-1/physiology , Humans , In Vitro Techniques , Kinetics , Lectins/chemistry , Lectins/pharmacokinetics , Mannose/chemistry , Mannosides/chemistry , Models, Molecular , Protein Structure, Tertiary
18.
Article in English | MEDLINE | ID: mdl-19478432

ABSTRACT

RNA 3'-terminal phosphate cyclase (Rtc) is an enzyme involved in RNA splicing that converts the 3'-terminal hydroxyl group of truncated RNA to 2',3'-cyclic phosphate, which is required just before its ligation. This reaction may occur in the following two steps: (i) Rtc + ATP --> Rtc-AMP + PP(i) and (ii) RNA-N3'p + Rtc-AMP --> RNA-N>p + Rtc + AMP. In order to reveal the reaction mechanism, Rtc of Sulfolobus tokodaii (St-Rtc) overexpressed in Escherichia coli was purified and crystallized in the following states: St-Rtc, St-Rtc+Mn, St-Rtc+ATP, St-Rtc+AMP and St-Rtc-AMP. The crystals diffracted to 2.25-3.00 A resolution and preliminary solutions of their structures have been obtained by molecular replacement using the structure of a selenomethionine-labelled St-Rtc crystal which was solved in advance using the MAD method as a model. These crystals grew in two different space groups (P3(1) and P4(2)), with the former space group displaying two distinct packing modes.


Subject(s)
Archaeal Proteins/chemistry , Ligases/chemistry , Sulfolobus/enzymology , Amino Acid Sequence , Apoenzymes/chemistry , Archaeal Proteins/isolation & purification , Buffers , Crenarchaeota/enzymology , Crystallization , Dimerization , Escherichia coli/genetics , Genetic Vectors , Hydrogen-Ion Concentration , Isoelectric Point , Ligases/isolation & purification , Ligases/metabolism , Models, Molecular , Molecular Sequence Data , Molecular Weight , Plasmids , Protein Conformation , Protein Structure, Secondary , Protein Structure, Tertiary , Rotation , Statistics as Topic , Transformation, Bacterial , X-Ray Diffraction
19.
Article in English | MEDLINE | ID: mdl-19342772

ABSTRACT

D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis catalyzes the reversible conversion between D-3-hydroxybutyrate and acetoacetate. The enzyme was crystallized in the presence of the substrate D-3-hydroxybutyrate and the cofactor NAD(+) at the optimum pH for the catalytic reaction. The structure, which was solved by X-ray crystallography, is isomorphous to that of the complex with the substrate analogue acetate. The product as well as the substrate molecule are accommodated well in the catalytic site. Their binding geometries suggest that the reversible reactions occur by shuttle movements of a hydrogen negative ion from the C3 atom of the substrate to the C4 atom of NAD(+) and from the C4 atom of NADH to the C3 atom of the product. The reaction might be further coupled to the withdrawal of a proton from the hydroxyl group of the substrate by the ionized Tyr155 residue. These structural features strongly support the previously proposed reaction mechanism of D-3-hydroxybutyrate dehydrogenase, which was based on the acetate-bound complex structure.


Subject(s)
Alcaligenes faecalis/enzymology , Hydroxybutyrate Dehydrogenase/chemistry , 3-Hydroxybutyric Acid/chemistry , Acetoacetates/chemistry , Biocatalysis , Coenzymes , Crystallography, X-Ray , Hydrophobic and Hydrophilic Interactions , NAD/chemistry , Static Electricity , Substrate Specificity
20.
Gene ; 437(1-2): 32-8, 2009 May 15.
Article in English | MEDLINE | ID: mdl-19374031

ABSTRACT

The yeast Ras-like small GTPases Gtr1p and Gtr2p form a heterodimer and interact genetically with Prp20p, a guanine nucleotide exchange factor for the GTPase Gsp1p. Gtr1p and Gtr2p may be involved in nucleocytoplasmic transport and in the nutrient-responsive TOR signaling pathway, but the role of the Gtr1p-Gtr2p heterodimer is not well understood. Characterization of the Gtr1p-Gtr2p complex is indispensable for understanding the functions of both Gtr1p and Gtr2p. We analyzed the association mode between Gtr1p and Gtr2p. The N-terminus nucleotide binding region of Gtr1p associated with Gtr2p, but not with Ego1p, a protein known to interact with Gtr1p. Gtr1p and Gtr2p are necessary for cells to acquire resistance to caffeine, rapamycin, and hydrogen peroxide. Caffeine treatment released Gtr1p from the high molecular weight Gtr1p-Gtr2p complex. Gtr2p mutants S23N and T44N, but not Q66L, rescued the gtr2 disruptant. Our findings indicate that the formation of heterodimers by Gtr1p differs between Gtr2p and Ego1p.


Subject(s)
Monomeric GTP-Binding Proteins/metabolism , Protein Multimerization , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Models, Molecular , Monomeric GTP-Binding Proteins/chemistry , Monomeric GTP-Binding Proteins/genetics , Point Mutation , Protein Interaction Mapping , Protein Serine-Threonine Kinases/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Signal Transduction
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