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Issue 12, 2009
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Dissection of USP catalytic domains reveals five common insertion points

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Abstract

Ubiquitin specific proteases (USPs) are the largest family of deubiquitinating enzymes with ∼56 members in humans. USPs regulate a wide variety of cellular processes by their ability to remove (poly)ubiquitin from target proteins. Their enzymatic activity is encoded in a common catalytic core of ∼350 amino acids, however many USPs show significantly larger catalytic domains. Here we have analysed human and yeast USP domains, combining bioinformatics with structural information. We reveal that all USP domains can be divided into six conserved boxes, and we map the conserved boxes onto the USP domain core structure. The boxes are interspersed by insertions, some of which as large as the catalytic core. The two most common insertion points place inserts near the distal ubiquitin binding site, and in many cases ubiquitin binding domains or ubiquitin-like folds are found in these insertions, potentially directly affecting catalytic function. Other inserted sequences are unstructured, and removal of these might aid future structural and functional analysis. Yeast USP domains have a different pattern of inserted sequences, suggesting that the insertions are hotspots for evolutionary diversity to expand USP functionality.

Graphical abstract: Dissection of USP catalytic domains reveals five common insertion points

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Publication details

The article was received on 16 Apr 2009, accepted on 05 Jun 2009, published on 17 Jul 2009 and first published online on 17 Jul 2009


Article type: Paper
DOI: 10.1039/B907669G
Citation: Mol. BioSyst., 2009,5, 1797-1808
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    Dissection of USP catalytic domains reveals five common insertion points

    Y. Ye, H. Scheel, K. Hofmann and D. Komander, Mol. BioSyst., 2009, 5, 1797
    DOI: 10.1039/B907669G

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