Structures of the otopetrin proton channels Otop1 and Otop3.

Abstract:

:Otopetrins (Otop1-Otop3) comprise one of two known eukaryotic proton-selective channel families. Otop1 is required for otoconia formation and a candidate mammalian sour taste receptor. Here we report cryo-EM structures of zebrafish Otop1 and chicken Otop3 in lipid nanodiscs. The structures reveal a dimeric architecture, with each subunit forming 12 transmembrane helices divided into structurally similar amino (N) and carboxy (C) domains. Cholesterol-like molecules occupy various sites in Otop1 and Otop3 and occlude a central tunnel. In molecular dynamics simulations, hydrophilic vestibules formed by the N and C domains and in the intrasubunit interface between N and C domains form conduits for water entry into the membrane core, suggesting three potential proton conduction pathways. By mutagenesis, we tested the roles of charged residues in each putative permeation pathway. Our results provide a structural basis for understanding selective proton permeation and gating of this conserved family of proton channels.

journal_name

Nat Struct Mol Biol

authors

Saotome K,Teng B,Tsui CCA,Lee WH,Tu YH,Kaplan JP,Sansom MSP,Liman ER,Ward AB

doi

10.1038/s41594-019-0235-9

subject

Has Abstract

pub_date

2019-06-01 00:00:00

pages

518-525

issue

6

eissn

1545-9993

issn

1545-9985

pii

10.1038/s41594-019-0235-9

journal_volume

26

pub_type

杂志文章
  • BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones.

    abstract::Small-molecule BET inhibitors interfere with the epigenetic interactions between acetylated histones and the bromodomains of the BET family proteins, including BRD4, and they potently inhibit growth of malignant cells by targeting cancer-promoting genes. BRD4 interacts with the pause-release factor P-TEFb and has been...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.2912

    authors: Kanno T,Kanno Y,LeRoy G,Campos E,Sun HW,Brooks SR,Vahedi G,Heightman TD,Garcia BA,Reinberg D,Siebenlist U,O'Shea JJ,Ozato K

    更新日期:2014-12-01 00:00:00

  • A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain.

    abstract::Argonaute (Ago) proteins mediate silencing of nucleic acid targets by small RNAs. In fission yeast, Ago1, Tas3 and Chp1 assemble into a RITS complex, which silences transcription near centromeres. Here we describe a repetitive motif within Tas3, termed the 'Argonaute hook', that is conserved from yeast to humans and b...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1302

    authors: Till S,Lejeune E,Thermann R,Bortfeld M,Hothorn M,Enderle D,Heinrich C,Hentze MW,Ladurner AG

    更新日期:2007-10-01 00:00:00

  • Reply to 'Misreading chaperone-substrate complexes from random noise'.

    abstract:: ...

    journal_title:Nature structural & molecular biology

    pub_type: 评论,信件

    doi:10.1038/s41594-018-0145-2

    authors: Horowitz S,Salmon L,Koldewey P,Ahlstrom LS,Martin R,Quan S,Afonine PV,van den Bedem H,Wang L,Xu Q,Trievel RC,Brooks CL 3rd,Bardwell JCA

    更新日期:2018-11-01 00:00:00

  • Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity.

    abstract::The Rbfox family of splicing factors regulate alternative splicing during animal development and in disease, impacting thousands of exons in the maturing brain, heart and muscle. Rbfox proteins have long been known to bind to the RNA sequence GCAUG with high affinity and specificity, but just half of Rbfox binding sit...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/s41594-020-0475-8

    authors: Begg BE,Jens M,Wang PY,Minor CM,Burge CB

    更新日期:2020-10-01 00:00:00

  • Conformational plasticity of the ClpAP AAA+ protease couples protein unfolding and proteolysis.

    abstract::The ClpAP complex is a conserved bacterial protease that unfolds and degrades proteins targeted for destruction. The ClpA double-ring hexamer powers substrate unfolding and translocation into the ClpP proteolytic chamber. Here, we determined high-resolution structures of wild-type Escherichia coli ClpAP undergoing act...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/s41594-020-0409-5

    authors: Lopez KE,Rizo AN,Tse E,Lin J,Scull NW,Thwin AC,Lucius AL,Shorter J,Southworth DR

    更新日期:2020-05-01 00:00:00

  • Transcription promotes contraction of CAG repeat tracts in human cells.

    abstract::Induced transcription through CAG repeats in human cells increases repeat contraction approximately 15-fold in both confluent and proliferating cells. Repeats are stabilized against contraction by siRNA knockdown of MSH2, MSH3 or XPA, but not by knockdown of MSH6, XPC or FEN1. These results define a pathway for CAG.CT...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1042

    authors: Lin Y,Dion V,Wilson JH

    更新日期:2006-02-01 00:00:00

  • Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing.

    abstract::We investigated whether a continuous transcript is necessary for co-transcriptional pre-mRNA processing. Cutting an intron with the fast-cleaving hepatitis delta ribozyme, but not the slower hammerhead, inhibited splicing. Therefore, exon tethering to RNA polymerase II (Pol II) cannot rescue splicing of a transcript s...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1652

    authors: Fong N,Ohman M,Bentley DL

    更新日期:2009-09-01 00:00:00

  • Interaction between the keratin cytoskeleton and eEF1Bgamma affects protein synthesis in epithelial cells.

    abstract::Eukaryotic elongation factor-1 (eEF1) is essential for peptide-chain elongation during translation. We report that its gamma subunit (eEF1Bgamma) specifically binds, and bundles, keratin intermediate filaments. Disrupting this interaction depresses translation by approximately 20% and selectively increases 80S ribosom...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1301

    authors: Kim S,Kellner J,Lee CH,Coulombe PA

    更新日期:2007-10-01 00:00:00

  • Structural insights into RNA processing by the human RISC-loading complex.

    abstract::Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Di...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1673

    authors: Wang HW,Noland C,Siridechadilok B,Taylor DW,Ma E,Felderer K,Doudna JA,Nogales E

    更新日期:2009-11-01 00:00:00

  • The opening of the two pores of the Hv1 voltage-gated proton channel is tuned by cooperativity.

    abstract::In voltage-gated sodium, potassium and calcium channels, the functions of ion conduction and voltage sensing are performed by two distinct structural units: the pore domain and the voltage-sensing domain (VSD). In the hydrogen voltage-gated channel 1 (Hv1), the VSD, unusually, performs both functions. Hv1 was recently...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1738

    authors: Tombola F,Ulbrich MH,Kohout SC,Isacoff EY

    更新日期:2010-01-01 00:00:00

  • Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease.

    abstract::DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5'-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5'-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx-DNA-AMP-Zn(2+) comple...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.2146

    authors: Tumbale P,Appel CD,Kraehenbuehl R,Robertson PD,Williams JS,Krahn J,Ahel I,Williams RS

    更新日期:2011-10-09 00:00:00

  • Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs.

    abstract::Flavin-containing monooxygenases (FMOs) are ubiquitous in all domains of life and metabolize a myriad of xenobiotics, including toxins, pesticides and drugs. However, despite their pharmacological importance, structural information remains bereft. To further our understanding behind their biochemistry and diversity, w...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/s41594-019-0347-2

    authors: Nicoll CR,Bailleul G,Fiorentini F,Mascotti ML,Fraaije MW,Mattevi A

    更新日期:2020-01-01 00:00:00

  • Translational control of the cytosolic stress response by mitochondrial ribosomal protein L18.

    abstract::In response to stress, cells attenuate global protein synthesis but permit efficient translation of mRNAs encoding heat-shock proteins (HSPs). Although decades have passed since the first description of the heat-shock response, how cells achieve translational control of HSP synthesis remains enigmatic. Here we report ...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.3010

    authors: Zhang X,Gao X,Coots RA,Conn CS,Liu B,Qian SB

    更新日期:2015-05-01 00:00:00

  • Structural basis for selective activation of ABA receptors.

    abstract::Changing environmental conditions and lessening fresh water supplies have sparked intense interest in understanding and manipulating abscisic acid (ABA) signaling, which controls adaptive responses to drought and other abiotic stressors. We recently discovered a selective ABA agonist, pyrabactin, and used it to discov...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1898

    authors: Peterson FC,Burgie ES,Park SY,Jensen DR,Weiner JJ,Bingman CA,Chang CE,Cutler SR,Phillips GN Jr,Volkman BF

    更新日期:2010-09-01 00:00:00

  • Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.

    abstract::Many genomic alterations associated with human diseases localize in noncoding regulatory elements located far from the promoters they regulate, making it challenging to link noncoding mutations or risk-associated variants with target genes. The range of action of a given set of enhancers is thought to be defined by in...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.2059

    authors: Martin D,Pantoja C,Fernández Miñán A,Valdes-Quezada C,Moltó E,Matesanz F,Bogdanović O,de la Calle-Mustienes E,Domínguez O,Taher L,Furlan-Magaril M,Alcina A,Cañón S,Fedetz M,Blasco MA,Pereira PS,Ovcharenko I,Recillas-Tar

    更新日期:2011-06-01 00:00:00

  • Nonsense-mediated mRNA decay occurs during eIF4F-dependent translation in human cells.

    abstract::The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs undergoing premature termination of translation. It has been argued that in human cells, NMD is restricted to a pioneer round of translation initiated on mRNAs associated with the cap-binding complex (CBC) and that the exchange of the CBC for the eIF4F tran...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.2575

    authors: Durand S,Lykke-Andersen J

    更新日期:2013-06-01 00:00:00

  • The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation.

    abstract::Aggregation of proteins containing polyglutamine (polyQ) expansions characterizes many neurodegenerative disorders, including Huntington's disease. Molecular chaperones modulate the aggregation and toxicity of the huntingtin (Htt) protein by an ill-defined mechanism. Here we determine how the chaperonin TRiC suppresse...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1700

    authors: Tam S,Spiess C,Auyeung W,Joachimiak L,Chen B,Poirier MA,Frydman J

    更新日期:2009-12-01 00:00:00

  • Transient ribosomal attenuation coordinates protein synthesis and co-translational folding.

    abstract::Clustered codons that pair to low-abundance tRNA isoacceptors can form slow-translating regions in the mRNA and cause transient ribosomal arrest. We report that folding efficiency of the Escherichia coli multidomain protein SufI can be severely perturbed by alterations in ribosome-mediated translational attenuation. S...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.1554

    authors: Zhang G,Hubalewska M,Ignatova Z

    更新日期:2009-03-01 00:00:00

  • Structural basis of tubulin detyrosination by vasohibins.

    abstract::Microtubules are regulated by post-translational modifications of tubulin. The ligation and cleavage of the carboxy-terminal tyrosine of α-tubulin impact microtubule functions during mitosis, cardiomyocyte contraction and neuronal processes. Tubulin tyrosination and detyrosination are mediated by tubulin tyrosine liga...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/s41594-019-0242-x

    authors: Li F,Hu Y,Qi S,Luo X,Yu H

    更新日期:2019-07-01 00:00:00

  • Catching DNA with hoops-biophysical approaches to clarify the mechanism of SMC proteins.

    abstract::Structural maintenance of chromosome (SMC) complexes are central regulators of chromosome architecture that are essential in all domains of life. For decades, the structural biology field has been debating how these conserved protein complexes use their intricate ring-like structures to structurally organize DNA. Here...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章,评审

    doi:10.1038/nsmb.3507

    authors: Eeftens J,Dekker C

    更新日期:2017-12-07 00:00:00

  • Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.

    abstract::Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the ...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb717

    authors: Sigel RK,Sashital DG,Abramovitz DL,Palmer AG,Butcher SE,Pyle AM

    更新日期:2004-02-01 00:00:00

  • The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle.

    abstract::The N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown. The crystal structure of the N-terminally acetylated BAH domain of Saccharomyces cerevisiae Sir3 bound to the nucleosome core particle reveals that the N-terminal acetylat...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.2641

    authors: Arnaudo N,Fernández IS,McLaughlin SH,Peak-Chew SY,Rhodes D,Martino F

    更新日期:2013-09-01 00:00:00

  • Structure of a purine-purine wobble base pair in the decoding center of the ribosome.

    abstract::Here we report the crystal structures of I.C and I.A wobble base pairs in the context of the ribosomal decoding center, clearly showing that the I.A base pair is of an I(anti).A(anti) conformation, as predicted by Crick. Additionally, the structures enable the observation of changes in the anticodon to allow purine-pu...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb866

    authors: Murphy FV 4th,Ramakrishnan V

    更新日期:2004-12-01 00:00:00

  • Regulation of MLL1 H3K4 methyltransferase activity by its core components.

    abstract::Histone H3 Lys4 (H3K4) methylation is a prevalent mark associated with transcription activation. A common feature of several H3K4 methyltransferase complexes is the presence of three structural components (RbBP5, Ash2L and WDR5) and a catalytic subunit containing a SET domain. Here we report the first biochemical reco...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1128

    authors: Dou Y,Milne TA,Ruthenburg AJ,Lee S,Lee JW,Verdine GL,Allis CD,Roeder RG

    更新日期:2006-08-01 00:00:00

  • BAK core dimers bind lipids and can be bridged by them.

    abstract::BAK and BAX are essential mediators of apoptosis that oligomerize in response to death cues, thereby causing permeabilization of the mitochondrial outer membrane. Their transition from quiescent monomers to pore-forming oligomers involves a well-characterized symmetric dimer intermediate. However, no essential seconda...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/s41594-020-0494-5

    authors: Cowan AD,Smith NA,Sandow JJ,Kapp EA,Rustam YH,Murphy JM,Brouwer JM,Bernardini JP,Roy MJ,Wardak AZ,Tan IK,Webb AI,Gulbis JM,Smith BJ,Reid GE,Dewson G,Colman PM,Czabotar PE

    更新日期:2020-11-01 00:00:00

  • SR protein kinases promote splicing of nonconsensus introns.

    abstract::Phosphorylation of the spliceosome is essential for RNA splicing, yet how and to what extent kinase signaling affects splicing have not been defined on a genome-wide basis. Using a chemical genetic approach, we show in Schizosaccharomyces pombe that the SR protein kinase Dsk1 is required for efficient splicing of intr...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb.3057

    authors: Lipp JJ,Marvin MC,Shokat KM,Guthrie C

    更新日期:2015-08-01 00:00:00

  • Proton-powered subunit rotation in single membrane-bound F0F1-ATP synthase.

    abstract::Synthesis of ATP from ADP and phosphate, catalyzed by F(0)F(1)-ATP synthases, is the most abundant physiological reaction in almost any cell. F(0)F(1)-ATP synthases are membrane-bound enzymes that use the energy derived from an electrochemical proton gradient for ATP formation. We incorporated double-labeled F(0)F(1)-...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb718

    authors: Diez M,Zimmermann B,Börsch M,König M,Schweinberger E,Steigmiller S,Reuter R,Felekyan S,Kudryavtsev V,Seidel CA,Gräber P

    更新日期:2004-02-01 00:00:00

  • Let K-Ras activate its own inhibitor.

    abstract:: ...

    journal_title:Nature structural & molecular biology

    pub_type: 新闻

    doi:10.1038/s41594-018-0066-0

    authors: Statsyuk AV

    更新日期:2018-06-01 00:00:00

  • Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d.

    abstract::The tandem zinc finger (TZF) domain of the protein TIS11d binds to the class II AU-rich element (ARE) in the 3' untranslated region (3' UTR) of target mRNAs and promotes their deadenylation and degradation. The NMR structure of the TIS11d TZF domain bound to the RNA sequence 5'-UUAUUUAUU-3' comprises a pair of novel C...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb738

    authors: Hudson BP,Martinez-Yamout MA,Dyson HJ,Wright PE

    更新日期:2004-03-01 00:00:00

  • Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells.

    abstract::Coupling between transcription and RNA processing is a key gene regulatory mechanism. Here we use chromatin immunoprecipitation to detect transcription-dependent accumulation of the precursor mRNA (pre-mRNA) splicing factors hnRNP A1, U2AF65 and U1 and U5 snRNPs on the intron-containing human FOS gene. These factors w...

    journal_title:Nature structural & molecular biology

    pub_type: 杂志文章

    doi:10.1038/nsmb1135

    authors: Listerman I,Sapra AK,Neugebauer KM

    更新日期:2006-09-01 00:00:00