About: Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4
Creator	Tanaka, Keiji Fukai, Shuya Okatsu, Kei Saeki, Yasushi Sato, Yusuke Tsuchiya, Hikaru Yamagata, Atsushi
Source	PMC
abstract	Npl4 is likely to be the most upstream factor recognizing Lys48-linked polyubiquitylated substrates in the proteasomal degradation pathway in yeast. Along with Ufd1, Npl4 forms a heterodimer (UN), and functions as a cofactor for the Cdc48 ATPase. Here, we report the crystal structures of yeast Npl4 in complex with Lys48-linked diubiquitin and with the Npl4-binding motif of Ufd1. The distal and proximal ubiquitin moieties of Lys48-linked diubiquitin primarily interact with the C-terminal helix and N-terminal loop of the Npl4 C-terminal domain (CTD), respectively. Mutational analysis suggests that the CTD contributes to linkage selectivity and initial binding of ubiquitin chains. Ufd1 occupies a hydrophobic groove of the Mpr1/Pad1 N-terminal (MPN) domain of Npl4, which corresponds to the catalytic groove of the MPN domain of JAB1/MPN/Mov34 metalloenzyme (JAMM)-family deubiquitylating enzyme. This study provides important structural insights into the polyubiquitin chain recognition by the Cdc48–UN complex and its assembly.
has issue date	2019-12-13(xsd:dateTime)
bibo:doi	10.1038/s41467-019-13697-y
bibo:pmid	31836717
has license	cc-by
sha1sum (hex)	aed0e70359bffd12f9748dc4d900d9ec3a170422
schema:url	https://doi.org/10.1038/s41467-019-13697-y
resource representing a document's title	Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4
has PubMed Central identifier	PMC6910952
has PubMed identifier	31836717
schema:publication	Nat Commun
resource representing a document's body	covid:aed0e70359bffd12f9748dc4d900d9ec3a170422#body_text
is schema:about of	named entity 'yeast' named entity 'motif' named entity 'insights' covid:arg/aed0e70359bffd12f9748dc4d900d9ec3a170422 named entity 'catalytic' named entity 'proximal' named entity 'functions' named entity 'distal' named entity 'JAMM' named entity 'chains' named entity 'ATPase' named entity 'structural' named entity 'initial' named entity 'ubiquitin' named entity 'domain' named entity 'C-terminal domain' named entity 'Structural' named entity 'heterodimer' named entity 'proximal' named entity 'distal' named entity 'JAB1' named entity 'Cdc48' named entity 'polyubiquitin' named entity 'CTD' named entity 'hydrophobic' named entity 'cofactor' named entity 'helix' named entity 'substrates' named entity 'spectroscopy' named entity 'Ponceau S' named entity 'NZF' named entity 'Tris-HCl' named entity 'ATP' named entity 'eluted' named entity 'SeMet' named entity 'Tris-HCl' named entity 'Phe' named entity 'Cdc48' named entity 'C-terminal tail' named entity 'EcoRI' named entity 'hydrophilic' named entity 'plasmon resonance' named entity 'E. coli' named entity 'pH 9' named entity 'crystallize' named entity 'Cdc48' named entity 'ATP hydrolysis' named entity '7.5' named entity 'thermophilum' named entity '2.55' named entity 'phenotype' named entity 'NaOH' named entity 'SeMet' named entity 'E. coli' named entity 'DTT' named entity 'UIM' named entity 'heterodimer' named entity 'substrate' named entity 'helix' named entity 'crystallization' named entity 'kanamycin' named entity 'UPS' named entity 'elution' named entity 'NaCl' named entity 'ATP hydrolysis' named entity 'SeMet' named entity 'expression vector' named entity 'ammonium acetate' named entity 'diffusion' named entity 'moiety' named entity 'Cdc48' named entity 'NZF' named entity 'diffusion' named entity 'ATP' named entity '7.5'

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