scholarly journals Allostery between two binding sites in the ion channel subunit TRIP8b confers binding specificity to HCN channels

2017 ◽  
Vol 292 (43) ◽  
pp. 17718-17730 ◽  
Author(s):  
Kyle A. Lyman ◽  
Ye Han ◽  
Robert J. Heuermann ◽  
Xiangying Cheng ◽  
Jonathan E. Kurz ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Cyclic Nucleotide ◽  
Tetratricopeptide Repeat ◽  
Hcn Channels ◽  
Protein Protein Interactions ◽  
C Terminus ◽  
Peroxisomal Targeting ◽  
Targeting Signal ◽  
Peroxisomal Targeting Signal

Tetratricopeptide repeat (TPR) domains are ubiquitous structural motifs that mediate protein–protein interactions. For example, the TPR domains in the peroxisomal import receptor PEX5 enable binding to a range of type 1 peroxisomal targeting signal motifs. A homolog of PEX5, tetratricopeptide repeat–containing Rab8b-interacting protein (TRIP8b), binds to and functions as an auxiliary subunit of hyperpolarization-activated cyclic nucleotide (HCN)–gated channels. Given the similarity between TRIP8b and PEX5, this difference in function raises the question of what mechanism accounts for their binding specificity. In this report, we found that the cyclic nucleotide–binding domain and the C terminus of the HCN channel are critical for conferring specificity to TRIP8b binding. We show that TRIP8b binds the HCN cyclic nucleotide–binding domain through a 37-residue domain and the HCN C terminus through the TPR domains. Using a combination of fluorescence polarization– and co-immunoprecipitation–based assays, we establish that binding at either site increases affinity at the other. Thus, allosteric coupling of the TRIP8b TPR domains both promotes binding to HCN channels and limits binding to type 1 peroxisomal targeting signal substrates. These results raise the possibility that other TPR domains may be similarly influenced by allosteric mechanisms as a general feature of protein–protein interactions.

scholarly journals Tetratricopeptide repeat domain of Yarrowia lipolytica Pex5p is essential for recognition of the type 1 peroxisomal targeting signal but does not confer full biological activity on Pex5p

2000 ◽  
Vol 346 (1) ◽  
pp. 177-184 ◽  
Author(s):  
Rachel K. SZILARD ◽  
Richard A. RACHUBINSKI
Keyword(s):  
Yarrowia Lipolytica ◽  
Tetratricopeptide Repeat ◽  
Binding Assays ◽  
Peroxisomal Targeting ◽  
Targeting Signal ◽  
Tetratricopeptide Repeat Domain ◽  
Tpr Domain ◽  
Peroxisomal Targeting Signal

Peroxins are proteins required for peroxisome assembly and are encoded by the PEX genes. The Yarrowia lipolytica pex5-1 mutant fails to import a subset of peroxisomal matrix proteins, including those with a type 1 peroxisomal targeting signal (PTS1). Pex5p family members interact with a PTS1 through their characteristic tetratricopeptide repeat (TPR) domain. We used binding assays in vitro to investigate the nature of the association of Y. lipolytica Pex5p (YlPex5p) with the PTS1 signal. A purified recombinant YlPex5p fusion protein interacted specifically, directly and autonomously with a protein terminating in a PTS1. Wild-type YlPex5p translated in vitro recognized functional PTS1s specifically. This activity is abrogated by the substitution of an aspartic residue for a conserved glycine residue in the TPR domain (G455D) of YlPex5p encoded by the pex5-1 allele. Deletion analysis demonstrated that an intact TPR domain of YlPex5p is necessary but not sufficient for both interaction with a PTS1 and functional complementation of a strain lacking YlPex5p.

scholarly journals Peroxisomal Targeting Signal Receptor Pex5p Interacts with Cargoes and Import Machinery Components in a Spatiotemporally Differentiated Manner: Conserved Pex5p WXXXF/Y Motifs Are Critical for Matrix Protein Import

2002 ◽  
Vol 22 (6) ◽  
pp. 1639-1655 ◽  
Author(s):  
Hidenori Otera ◽  
Kiyoko Setoguchi ◽  
Maho Hamasaki ◽  
Toshitaka Kumashiro ◽  
Nobuhiro Shimizu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Matrix Protein ◽  
Protein Import ◽  
Tetratricopeptide Repeat ◽  
Amino Acid Residues ◽  
Peroxisomal Targeting ◽  
Signal Type ◽  
Targeting Signal ◽  
Peroxisomal Targeting Signal

ABSTRACT Two isoforms of the peroxisomal targeting signal type 1 (PTS1) receptor, termed Pex5pS and (37-amino-acid-longer) Pex5pL, are expressed in mammals. Pex5pL transports PTS1 proteins and Pex7p-PTS2 cargo complexes to the initial Pex5p-docking site, Pex14p, on peroxisome membranes, while Pex5pS translocates only PTS1 cargoes. Here we report functional Pex5p domains responsible for interaction with peroxins Pex7p, Pex13p, and Pex14p. An N-terminal half, such as Pex5pL(1-243), comprising amino acid residues 1 to 243, bound to Pex7p, Pex13p, and Pex14p and was sufficient for restoring the impaired PTS2 import of pex5 cell mutants, while the C-terminal tetratricopeptide repeat motifs were required for PTS1 binding. N-terminal Pex5p possessed multiple Pex14p-binding sites. Alanine-scanning analysis of the highly conserved seven (six in Pex5pS) pentapeptide WXXXF/Y motifs residing at the N-terminal region indicated that these motifs were essential for the interaction of Pex5p with Pex14p and Pex13p. Moreover, mutation of several WXXXF/Y motifs did not affect the PTS import-restoring activity of Pex5p, implying that the binding of Pex14p to all of the WXXXF/Y sites was not a prerequisite for the translocation of Pex5p-cargo complexes. Pex5p bound to Pex13p at the N-terminal part, not to the C-terminal SH3 region, via WXXXF/Y motifs 2 to 4. PTS1 and PTS2 import required the interaction of Pex5p with Pex14p but not with Pex13p, while Pex5p binding to Pex13p was essential for import of catalase with PTS1-like signal KANL. Pex5p recruited PTS1 proteins to Pex14p but not to Pex13p. Pex14p and Pex13p formed a complex with PTS1-loaded Pex5p but dissociated in the presence of cargo-unloaded Pex5p, implying that PTS cargoes are released from Pex5p at a step downstream of Pex14p and upstream of Pex13p. Thus, Pex14p and Pex13p very likely form mutually and temporally distinct subcomplexes involved in peroxisomal matrix protein import.

scholarly journals In SilicoAnalysis ofArabidopsis thalianaPeroxisomal 6-Phosphogluconate Dehydrogenase

Scientifica ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Álvaro D. Fernández-Fernández ◽  
Francisco J. Corpas
Keyword(s):  
Gene Expression ◽  
In Silico ◽  
Redox Homeostasis ◽  
Affymetrix Microarray ◽  
Phosphogluconate Dehydrogenase ◽  
Peroxisomal Targeting ◽  
Targeting Signal ◽  
Xenobiotic Response ◽  
Peroxisomal Targeting Signal

NADPH, whose regeneration is critical for reductive biosynthesis and detoxification pathways, is an essential component in cell redox homeostasis. Peroxisomes are subcellular organelles with a complex biochemical machinery involved in signaling and stress processes by molecules such as hydrogen peroxide (H2O2) and nitric oxide (NO). NADPH is required by several peroxisomal enzymes involved inβ-oxidation, NO, and glutathione (GSH) generation. Plants have various NADPH-generating dehydrogenases, one of which is 6-phosphogluconate dehydrogenase (6PGDH). Arabidopsis contains three6PGDHgenes that probably are encoded for cytosolic, chloroplastic/mitochondrial, and peroxisomal isozymes, although their specific functions remain largely unknown. This study focuses on thein silicoanalysis of the biochemical characteristics and gene expression of peroxisomal 6PGDH (p6PGDH) with the aim of understanding its potential function in the peroxisomal NADPH-recycling system. The data show that a group of plant 6PGDHs contains an archetypal type 1 peroxisomal targeting signal (PTS), whilein silicogene expression analysis using affymetrix microarray data suggests that Arabidopsis p6PGDH appears to be mainly involved in xenobiotic response, growth, and developmental processes.

scholarly journals Recognition of Peroxisomal Targeting Signal Type 1 by the Import Receptor Pex5p

2001 ◽  
Vol 276 (18) ◽  
pp. 15034-15041 ◽  
Author(s):  
André T. J. Klein ◽  
Phil Barnett ◽  
Gina Bottger ◽  
Daphne Konings ◽  
Henk F. Tabak ◽  
...  
Keyword(s):  
Peroxisomal Targeting ◽  
Signal Type ◽  
Targeting Signal ◽  
Peroxisomal Targeting Signal ◽  
Import Receptor

scholarly journals Pex13p is an SH3 protein of the peroxisome membrane and a docking factor for the predominantly cytoplasmic PTs1 receptor.

1996 ◽  
Vol 135 (1) ◽  
pp. 85-95 ◽  
Author(s):  
S J Gould ◽  
J E Kalish ◽  
J C Morrell ◽  
J Bjorkman ◽  
A J Urquhart ◽  
...  
Keyword(s):  
Steady State ◽  
Matrix Proteins ◽  
Cytoplasmic Protein ◽  
Peroxisomal Membrane ◽  
Peroxisomal Targeting ◽  
Targeting Signal ◽  
Peroxisome Membrane ◽  
Peroxisomal Targeting Signal

Import of newly synthesized PTS1 proteins into the peroxisome requires the PTS1 receptor (Pex5p), a predominantly cytoplasmic protein that cycles between the cytoplasm and peroxisome. We have identified Pex13p, a novel integral peroxisomal membrane from both yeast and humans that binds the PTS1 receptor via a cytoplasmically oriented SH3 domain. Although only a small amount of Pex5p is bound to peroxisomes at steady state (< 5%), loss of Pex13p further reduces the amount of peroxisome-associated Pex5p by approximately 40-fold. Furthermore, loss of Pex13p eliminates import of peroxisomal matrix proteins that contain either the type-1 or type-2 peroxisomal targeting signal but does not affect targeting and insertion of integral peroxisomal membrane proteins. We conclude that Pex13p functions as a docking factor for the predominantly cytoplasmic PTS1 receptor.

scholarly journals Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Fabian Schueren ◽  
Thomas Lingner ◽  
Rosemol George ◽  
Julia Hofhuis ◽  
Corinna Dickel ◽  
...  
Keyword(s):  
Lactate Dehydrogenase ◽  
In Silico ◽  
Stop Codon ◽  
The Other ◽  
Translational Readthrough ◽  
Peroxisomal Targeting ◽  
Signal Type ◽  
Targeting Signal ◽  
Peroxisomal Targeting Signal

Translational readthrough gives rise to low abundance proteins with C-terminal extensions beyond the stop codon. To identify functional translational readthrough, we estimated the readthrough propensity (RTP) of all stop codon contexts of the human genome by a new regression model in silico, identified a nucleotide consensus motif for high RTP by using this model, and analyzed all readthrough extensions in silico with a new predictor for peroxisomal targeting signal type 1 (PTS1). Lactate dehydrogenase B (LDHB) showed the highest combined RTP and PTS1 probability. Experimentally we show that at least 1.6% of the total cellular LDHB is targeted to the peroxisome by a conserved hidden PTS1. The readthrough-extended lactate dehydrogenase subunit LDHBx can also co-import LDHA, the other LDH subunit, into peroxisomes. Peroxisomal LDH is conserved in mammals and likely contributes to redox equivalent regeneration in peroxisomes.

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