A data set of human endogenous protein ubiquitination sites.
Lysine ubiquitination is an important and versatile protein post-translational modification. Numerous cellular functions are regulated by ubiquitination, suggesting that extensive numbers of proteins, if not all, are modified with ubiquitin at certain times. However, proteome-wide profiling of ubiquitination sites in the mammalian system is technically challenging. We report the design and characterization of an engineered protein affinity reagent for the isolation of ubiquitinated proteins and the identification of ubiquitination sites with mass spectrometry. This recombinant protein consists of four tandem repeats of ubiquitin-associated domain from UBQLN1 fused to a GST tag. We used this GST-qUBA reagent to isolate polyubiquitinated proteins and identified 294 endogenous ubiquitination sites on 223 proteins from human 293T cells without proteasome inhibitors or overexpression of ubiquitin. Mitochondrial proteins constitute 14.7% of this data set, implicating ubiquitination in a wide range of mitochondrial functions.
Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
Yi
Y
Shi
Doug W
DW
Chan
Sung Yun
SY
Jung
Anna
A
Malovannaya
Yi
Y
Wang
Jun
J
Qin
D000465:Algorithms; D020816:Amino Acid Motifs; D002352:Carrier Proteins / Q000737:chemistry*; D002853:Chromatography, Liquid / Q000379:methods; D057809:HEK293 Cells; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry / Q000378:metabolism; D008970:Molecular Weight; D011485:Protein Binding; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D011993:Recombinant Fusion Proteins / Q000737:chemistry*; D053719:Tandem Mass Spectrometry; D025521:Tumor Suppressor Proteins / Q000737:chemistry / Q000378:metabolism; D057149:Ubiquitinated Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D054875:Ubiquitination
D002352:Carrier Proteins; D047908:Intracellular Signaling Peptides and Proteins; D020543:Proteome; D011993:Recombinant Fusion Proteins; D025521:Tumor Suppressor Proteins; D057149:Ubiquitinated Proteins