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The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages.

Altun M, Walter TS, Kramer HB, Herr P, Iphöfer A, Boström J, David Y, Komsany A, Ternette N, Navon A, Stuart DI, Ren J, Kessler BM - PLoS ONE (2015)

Bottom Line: The ubiquitin binding mode is oriented differently to how viral otubains (vOTUs) bind ubiquitin/ISG15, and more similar to yeast and mammalian OTUs.In contrast to OTUB1 which has exclusive specificity towards Lys48 poly-ubiquitin chains, OTUB2 cleaves different poly-Ub linked chains.N-terminal tail swapping experiments between OTUB1 and OTUB2 revealed how the N-terminal structural motifs in OTUB1 contribute to modulating enzyme activity and Ub-chain selectivity, a trait not observed in OTUB2, supporting the notion that OTUB2 may affect a different spectrum of substrates in Ub-dependent pathways.

View Article: PubMed Central - PubMed

Affiliation: Target Discovery Institute, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, Oxford, OX3 7FZ, United Kingdom; Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21 Stockholm, Sweden.

ABSTRACT
Ovarian tumor domain containing proteases cleave ubiquitin (Ub) and ubiquitin-like polypeptides from proteins. Here we report the crystal structure of human otubain 2 (OTUB2) in complex with a ubiquitin-based covalent inhibitor, Ub-Br2. The ubiquitin binding mode is oriented differently to how viral otubains (vOTUs) bind ubiquitin/ISG15, and more similar to yeast and mammalian OTUs. In contrast to OTUB1 which has exclusive specificity towards Lys48 poly-ubiquitin chains, OTUB2 cleaves different poly-Ub linked chains. N-terminal tail swapping experiments between OTUB1 and OTUB2 revealed how the N-terminal structural motifs in OTUB1 contribute to modulating enzyme activity and Ub-chain selectivity, a trait not observed in OTUB2, supporting the notion that OTUB2 may affect a different spectrum of substrates in Ub-dependent pathways.

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Comparison of OTUB2-Ub and OTUB1-Ubal-UBCH5B-Ub complexes.(A) Overlay of OTUB2-Ub (blue and red) and OTUB1-Ubal-UBCH5B-Ub (grey, grey, cyan and orange respectively) complexes. The N-terminal helix of OTUB1 is shown in magenta for clarity. Side-chains from OTUB1 and the proximal Ub are shown as sticks; black broken lines represent hydrogen bonds, and the red sphere a water molecule. (B) The N-terminal of OTUB2 is shorter and folded to a different direction compared to OTUB1. (C) Close up view of the interactions between the proximal Ub and the OTUB1 α2α3 loop which is two residue shorter in OTUB2 (α1α2 loop).
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pone.0115344.g004: Comparison of OTUB2-Ub and OTUB1-Ubal-UBCH5B-Ub complexes.(A) Overlay of OTUB2-Ub (blue and red) and OTUB1-Ubal-UBCH5B-Ub (grey, grey, cyan and orange respectively) complexes. The N-terminal helix of OTUB1 is shown in magenta for clarity. Side-chains from OTUB1 and the proximal Ub are shown as sticks; black broken lines represent hydrogen bonds, and the red sphere a water molecule. (B) The N-terminal of OTUB2 is shorter and folded to a different direction compared to OTUB1. (C) Close up view of the interactions between the proximal Ub and the OTUB1 α2α3 loop which is two residue shorter in OTUB2 (α1α2 loop).

Mentions: A striking difference between OTUB1 and OTUB2 is the N-terminal domain length and architecture. In the complex structure of OTUB1-Ub-UBCH5b-Ub, the proximal Ub makes extensive interactions with the N-terminal helix and α1α2 loop of OTUB1 [13–15], and the interaction with the E2 (UBC13) helps stabilizing the N-terminal α-helix [15] (Figs. 3C and 4A). The shorter N-terminal tail of OTUB2 is unstructured and oriented away from proximal ubiquitin (Fig. 4B). Notably, in the case of OTUB1, the residues Thr61 and Ser62 in the N-terminal α2α3 loop interact with proximal Ub through a hydrogen bond network with Gln62 and Asn60 (Fig. 4C). Since OTUB2 does not have the N-terminal helix and its α1α2 loop is 2 residues shorter, it is expected that the binding of proximal Ub to OTUB2 is substantially different from OTUB1.


The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages.

Altun M, Walter TS, Kramer HB, Herr P, Iphöfer A, Boström J, David Y, Komsany A, Ternette N, Navon A, Stuart DI, Ren J, Kessler BM - PLoS ONE (2015)

Comparison of OTUB2-Ub and OTUB1-Ubal-UBCH5B-Ub complexes.(A) Overlay of OTUB2-Ub (blue and red) and OTUB1-Ubal-UBCH5B-Ub (grey, grey, cyan and orange respectively) complexes. The N-terminal helix of OTUB1 is shown in magenta for clarity. Side-chains from OTUB1 and the proximal Ub are shown as sticks; black broken lines represent hydrogen bonds, and the red sphere a water molecule. (B) The N-terminal of OTUB2 is shorter and folded to a different direction compared to OTUB1. (C) Close up view of the interactions between the proximal Ub and the OTUB1 α2α3 loop which is two residue shorter in OTUB2 (α1α2 loop).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4295869&req=5

pone.0115344.g004: Comparison of OTUB2-Ub and OTUB1-Ubal-UBCH5B-Ub complexes.(A) Overlay of OTUB2-Ub (blue and red) and OTUB1-Ubal-UBCH5B-Ub (grey, grey, cyan and orange respectively) complexes. The N-terminal helix of OTUB1 is shown in magenta for clarity. Side-chains from OTUB1 and the proximal Ub are shown as sticks; black broken lines represent hydrogen bonds, and the red sphere a water molecule. (B) The N-terminal of OTUB2 is shorter and folded to a different direction compared to OTUB1. (C) Close up view of the interactions between the proximal Ub and the OTUB1 α2α3 loop which is two residue shorter in OTUB2 (α1α2 loop).
Mentions: A striking difference between OTUB1 and OTUB2 is the N-terminal domain length and architecture. In the complex structure of OTUB1-Ub-UBCH5b-Ub, the proximal Ub makes extensive interactions with the N-terminal helix and α1α2 loop of OTUB1 [13–15], and the interaction with the E2 (UBC13) helps stabilizing the N-terminal α-helix [15] (Figs. 3C and 4A). The shorter N-terminal tail of OTUB2 is unstructured and oriented away from proximal ubiquitin (Fig. 4B). Notably, in the case of OTUB1, the residues Thr61 and Ser62 in the N-terminal α2α3 loop interact with proximal Ub through a hydrogen bond network with Gln62 and Asn60 (Fig. 4C). Since OTUB2 does not have the N-terminal helix and its α1α2 loop is 2 residues shorter, it is expected that the binding of proximal Ub to OTUB2 is substantially different from OTUB1.

Bottom Line: The ubiquitin binding mode is oriented differently to how viral otubains (vOTUs) bind ubiquitin/ISG15, and more similar to yeast and mammalian OTUs.In contrast to OTUB1 which has exclusive specificity towards Lys48 poly-ubiquitin chains, OTUB2 cleaves different poly-Ub linked chains.N-terminal tail swapping experiments between OTUB1 and OTUB2 revealed how the N-terminal structural motifs in OTUB1 contribute to modulating enzyme activity and Ub-chain selectivity, a trait not observed in OTUB2, supporting the notion that OTUB2 may affect a different spectrum of substrates in Ub-dependent pathways.

View Article: PubMed Central - PubMed

Affiliation: Target Discovery Institute, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, Oxford, OX3 7FZ, United Kingdom; Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21 Stockholm, Sweden.

ABSTRACT
Ovarian tumor domain containing proteases cleave ubiquitin (Ub) and ubiquitin-like polypeptides from proteins. Here we report the crystal structure of human otubain 2 (OTUB2) in complex with a ubiquitin-based covalent inhibitor, Ub-Br2. The ubiquitin binding mode is oriented differently to how viral otubains (vOTUs) bind ubiquitin/ISG15, and more similar to yeast and mammalian OTUs. In contrast to OTUB1 which has exclusive specificity towards Lys48 poly-ubiquitin chains, OTUB2 cleaves different poly-Ub linked chains. N-terminal tail swapping experiments between OTUB1 and OTUB2 revealed how the N-terminal structural motifs in OTUB1 contribute to modulating enzyme activity and Ub-chain selectivity, a trait not observed in OTUB2, supporting the notion that OTUB2 may affect a different spectrum of substrates in Ub-dependent pathways.

Show MeSH
Related in: MedlinePlus