The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

Pearl, Frances M. G.; Todd, Alan K.; Sillitoe, Ian; Dibley, Mark; Redfern, Oliver; Lewis, Tony E.; Bennett, Christopher; Marsden, Russell L.; Grant, Alastair; Lee, David A.; Akpor, Adrian; Maibaum, Michael; Harrison, Andrew; Dallman, Timothy J.; Reeves, Gabrielle A.; Diboun, Ilhem; Addou, S.; Lise, Stefano; Johnston, Caroline; Sillero, Antonio; Thornton, Janet M.; Orengo, Christine A.

doi:10.1093/nar/gki024

Cited by 237 publications

(173 citation statements)

References 22 publications

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“…The β-subunit of the Na + -channel has an Ig-fold domain in the extracellular region and was demonstrated to be involved in cell-cell adhesion via a direct interaction with the extracellular matrix (Srinivasan et al, 1998;Undrovinas et al, 1995;Xiao et al, 1999). Recent bioinformatic analysis and x-ray crystallography demonstrated that the Ig-fold structure can be found in various proteins (Halaby et al, 1999;Pearl et al, 2005). Each Ig fold is composed of sequential and antiparallel short β-sheets, some of which are relatively hydrophobic (Halaby et al, 1999).…”

Section: Possible Involvement Of the β-Subunit In Cell-cell Adhesionmentioning

confidence: 99%

Fast degradation of the auxiliary subunit of Na+/K+-ATPase in the plasma membrane of HeLa cells

Yoshimura

Iwasaka

Schwarz

2008

Journal of Cell Science

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The cell-surface expression and function of multisubunit plasma membrane proteins are regulated via interactions between catalytic subunits and auxiliary subunits. Subunit assembly in the endoplasmic reticulum is required for the cell-surface expression of the enzyme, but little is known about subunit interactions once it reaches the plasma membrane. Here we performed highly quantitative analyses of the catalytic (α1) and auxiliary (β1 and β3) subunits of Na+/K+-ATPase in the HeLa cell plasma membrane using isoform-specific antibodies and a cell-surface protein labeling procedure. Our results indicate that although the β-subunit is required for the cell-surface expression of the α-subunit, the plasma membrane contains more α-subunits than β-subunits. Pulse-labeling and chasing of the cell-surface proteins revealed that degradation of the β-subunits was much faster than that of the α1-subunit. Ubiquitylation, as well as endocytosis, was involved in the fast degradation of the β1-subunit. Double knockdown of the β1- and β3-subunits by RNAi resulted in the disappearance of these β-subunits but not the α1-subunit in the plasma membrane. All these results indicate that the α- and β-subunits of Na+/K+-ATPase are assembled in the endoplasmic reticulum, but are disassembled in the plasma membrane and undergo different degradation processes.

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Section: Possible Involvement Of the β-Subunit In Cell-cell Adhesionmentioning

confidence: 99%

Fast degradation of the auxiliary subunit of Na+/K+-ATPase in the plasma membrane of HeLa cells

Yoshimura

Iwasaka

Schwarz

2008

Journal of Cell Science

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“…In spite of the low sequence identity, usually below 10%, PRYSPRY and the proteins of the top DALI hits share the same core b-sandwich architecture, that of a jelly roll topology (CATH, [31]). Interestingly, in pea lectin [30], a homologue of the CRD of p58/ERGIC-53, an extended binding pocket is located on the concave side of the b-sheet as we see in the PRYSPRY-domain (Fig.…”

Section: Fold Comparison With Other Proteinsmentioning

confidence: 99%

Structure of the PRYSPRY‐domain: Implications for autoinflammatory diseases

et al. 2005

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We determined the first structure of PRYSPRY, a domain found in over 500 different proteins, involved in innate immune signaling, cytokine signaling suppression, development, cell growth and retroviral restriction. The fold encompasses a 7-stranded and a 6-stranded antiparallel b-sheet, arranged in a b-sandwich. In the crystal, PRYSPRY forms a dimer where the C-terminus of an acceptor molecule binds to the concave surface of a donor molecule, which represents a putative interaction site. Mutations in the PRYSPRY domains of Pyrin, which are responsible for familial Mediterranean fever, map on the putative PRYSPRY interaction site.

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“…CATH server classified the protein as alpha beta with a 2-layer sandwich architecture and topology similar to double stranded RNA binding domain (Pearl et al, 2004). The overall structure consists of 3 helices and 3 sheets.…”

Section: Introductionmentioning

confidence: 99%

Crystal structure of a novel non-Pfam protein PF2046 solved using low resolution B-factor sharpening and multi-crystal averaging methods

Shaw

et al. 2010

Protein Cell

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Sometimes crystals cannot diffract X-rays beyond 3.0 Å resolution due to the intrinsic flexibility associated with the protein. Low resolution diffraction data not only pose a challenge to structure determination, but also hamper interpretation of mechanistic details. Crystals of a 25.6 kDa non-Pfam, hypothetical protein, PF2046, diffracted X-rays to 3.38 Å resolution. A combination of SeMet derived heavy atom positions with multiple cycles of B-factor sharpening, multi-crystal averaging, restrained refinement followed by manual inspection of electron density and model building resulted in a final model with a R value of 23.5 (R free = 24.7). The asymmetric unit was large and consisted of six molecules arranged as a homodimer of trimers. Analysis of the structure revealed the presence of a RNA binding domain suggesting a role for PF2046 in the processing of nucleic acids.

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The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

Cited by 237 publications

References 22 publications

Fast degradation of the auxiliary subunit of Na+/K+-ATPase in the plasma membrane of HeLa cells

Fast degradation of the auxiliary subunit of Na+/K+-ATPase in the plasma membrane of HeLa cells

Structure of the PRYSPRY‐domain: Implications for autoinflammatory diseases

Crystal structure of a novel non-Pfam protein PF2046 solved using low resolution B-factor sharpening and multi-crystal averaging methods

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