Data in support of UbSRD: The Ubiquitin Structural Relational Database

Joseph S. Harrison, Tim M. Jacobs, Kevin Houlihan, Koenraad Van Doorslaer, Brian Kuhlman

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Abstract

This article provides information to support the database article titled "UbSRD: The Ubiquitin Structural Relational Database" (Harrison et al., 2015) [1] The ubiquitin-like homology fold (UBL) represents a large family that encompasses both post-translational modifications, like ubiquitin (UBQ) and SUMO, and functional domains on many biologically important proteins like Parkin, UHRF1 (ubiquitin-like with PDB and RING finger domains-1), and Usp7 (ubiquitin-specific protease-7) (Zhang et al., 2015; Rothbart et al., 2013; Burroughs et al., 2012; Wauer et al., 2015) [2-5]. The UBL domain can participate in several unique protein-protein interactions (PPI) since protein adducts can be attached to and removed from amino groups of lysine side chains and the N-terminus of proteins. Given the biological significance of UBL domains, many have been characterized with high-resolution techniques, and for UBQ and SUMO, many protein complexes have been characterized. We identified all the UBL domains in the PDB and created a relational database called UbSRD (Ubiquitin Structural Relational Database) by using structural analysis tools in the Rosetta (Leaver et al., 2013; O'Meara et al., 2015; Leaver-fay et al., 2011) [1,6-8]. Querying UbSRD permitted us to report many quantitative properties of UBQ and SUMO recognition at different types interfaces (noncovalent: NC, conjugated: CJ, and deubiquitanse: DB). In this data article, we report the average number of non-UBL neighbors, secondary structure of interacting motifs, and the type of inter-molecular hydrogen bonds for each residue of UBQ and SUMO. Additionally, we used PROMALS3D to generate a multiple sequence alignment used to construct a phylogram for the entire set of UBLs (Pei and Grishin, 2014) [9]. The data described here will be generally useful to scientists studying the molecular basis for recognition of UBQ or SUMO.

Original languageEnglish (US)
Pages (from-to)605-615
Number of pages11
JournalData in Brief
Volume5
DOIs
StatePublished - Dec 1 2015
Externally publishedYes

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large family
structural analysis
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Data in support of UbSRD : The Ubiquitin Structural Relational Database. / Harrison, Joseph S.; Jacobs, Tim M.; Houlihan, Kevin; Van Doorslaer, Koenraad; Kuhlman, Brian.

In: Data in Brief, Vol. 5, 01.12.2015, p. 605-615.

Research output: Contribution to journalArticle

Harrison, Joseph S. ; Jacobs, Tim M. ; Houlihan, Kevin ; Van Doorslaer, Koenraad ; Kuhlman, Brian. / Data in support of UbSRD : The Ubiquitin Structural Relational Database. In: Data in Brief. 2015 ; Vol. 5. pp. 605-615.
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