2008
DOI: 10.1074/jbc.m704398200
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Abstract: Ubiquitination of proteins modifies protein function by either altering their activities, promoting their degradation, or altering their subcellular localization. Deubiquitinating enzymes are proteases that reverse this ubiquitination. Previous studies demonstrate that proteins that contain an ovarian tumor (OTU) domain possess deubiquitinating activity. This domain of ϳ130 amino acids is weakly similar to the papain family of proteases and is highly conserved from yeast to mammals. Here we report structural a… Show more

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Cited by 98 publications
(141 citation statements)
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“…The N1 domain (residues 23-104) consists of a double-⌿ ␤-barrel, and the N2 domain (residues 112-196) consists of a six-stranded ␤-clam with two helices on the two ends as described earlier (7). The structure of UBXL OTU1 (residues 1-73) reveals a ␤-grasp fold with a ␤-␤-␣-␤-␤-␣-␣-␤ secondary structural organization that resembles ubiquitin and ubiquitin-like proteins as well as UBX and the ubiquitin D domain (UBD) (18,32). However, it differs significantly, especially in the conformation of the loops and the electrostatic surface, and these differences will be discussed later.…”
Section: Resultsmentioning
confidence: 99%
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“…The N1 domain (residues 23-104) consists of a double-⌿ ␤-barrel, and the N2 domain (residues 112-196) consists of a six-stranded ␤-clam with two helices on the two ends as described earlier (7). The structure of UBXL OTU1 (residues 1-73) reveals a ␤-grasp fold with a ␤-␤-␣-␤-␤-␣-␣-␤ secondary structural organization that resembles ubiquitin and ubiquitin-like proteins as well as UBX and the ubiquitin D domain (UBD) (18,32). However, it differs significantly, especially in the conformation of the loops and the electrostatic surface, and these differences will be discussed later.…”
Section: Resultsmentioning
confidence: 99%
“…However, UBXL has low sequence identity of less than 15% to UBX and furthermore lacks the signature motif of UBX. So far, the structure of the OTU domain from yeast complexed with ubiquitin has been produced (18), and recently it has been demonstrated that YOD1, the mammalian homolog of OTU1, has high specificity for Lys 11 -linked ubiquitin chains in a report that shows the complex structure of YOD1 with Lys 11 -linked diubiquitin (19). To understand how OTU1 interacts with VCP on a molecular level and to gain insight into how this interaction regulates the ERAD pathway, we carried out a structural study on N VCP complexed with UBXL OTU1 and performed negative staining electron microscopy (EM) and biochemical studies of the full-length proteins.…”
mentioning
confidence: 99%
“…Atg4B is an essential enzyme in autophagy that cleaves nascent Atg8 at its C-terminal arginine residue and deconjugates Atg8 family proteins from a small adduct, phosphatidylethanolamine (12). Other deubiquitinating enzymes such as USP14 (PDB code 2AYN) (13) and OTU1(PDB code 3C0R) (14) had much lower Z-scores, 4.6 and 3.6, respectively. When the N-terminal domain of UfSP2 alone was tested, there were no significant hits on structural similarity search using either DALI or TM-align (15).…”
Section: Resultsmentioning
confidence: 99%
“…1B). Rsp5 does not carry any of the numerous UBDs that have been described to date (6,(35)(36)(37). To test which region of the Rsp5 protein is responsible for its ubiquitin-binding activity, we assayed different fragments of Rsp5 for binding to ubiquitin-agarose beads.…”
Section: Resultsmentioning
confidence: 99%