Structural Basis of the Specificity of USP18 Toward ISG15

Overview

Journal Nat Struct Mol Biol

Specialties Cell Biology
Molecular Biology

Date 2017 Feb 7

PMID 28165509

Citations 61

Authors

Anja Basters

Paul P Geurink

Annika Rocker

Katharina F Witting

Roya Tadayon

Sandra Hess

Marta S Semrau

Paola Storici

Huib Ovaa

Klaus-Peter Knobeloch

Gunter Fritz

Affiliations

Soon will be listed here.

Abstract

Protein modification by ubiquitin and ubiquitin-like modifiers (Ubls) is counteracted by ubiquitin proteases and Ubl proteases, collectively termed DUBs. In contrast to other proteases of the ubiquitin-specific protease (USP) family, USP18 shows no reactivity toward ubiquitin but specifically deconjugates the interferon-induced Ubl ISG15. To identify the molecular determinants of this specificity, we solved the crystal structures of mouse USP18 alone and in complex with mouse ISG15. USP18 was crystallized in an open and a closed conformation, thus revealing high flexibility of the enzyme. Structural data, biochemical and mutational analysis showed that only the C-terminal ubiquitin-like domain of ISG15 is recognized and essential for USP18 activity. A critical hydrophobic patch in USP18 interacts with a hydrophobic region unique to ISG15, thus providing evidence that USP18's ISG15 specificity is mediated by a small interaction interface. Our results may provide a structural basis for the development of new drugs modulating ISG15 linkage.

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References

Zou W, Papov V, Malakhova O, Kim K, Dao C, Li J . ISG15 modification of ubiquitin E2 Ubc13 disrupts its ability to form thioester bond with ubiquitin. Biochem Biophys Res Commun. 2005; 336(1):61-8. DOI: 10.1016/j.bbrc.2005.08.038. View

Waterhouse A, Procter J, Martin D, Clamp M, Barton G . Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009; 25(9):1189-91. PMC: 2672624. DOI: 10.1093/bioinformatics/btp033. View

Oudshoorn D, van Boheemen S, Sanchez-Aparicio M, Rajsbaum R, Garcia-Sastre A, Versteeg G . HERC6 is the main E3 ligase for global ISG15 conjugation in mouse cells. PLoS One. 2012; 7(1):e29870. PMC: 3260183. DOI: 10.1371/journal.pone.0029870. View

Zhang X, Bogunovic D, Payelle-Brogard B, Francois-Newton V, Speer S, Yuan C . Human intracellular ISG15 prevents interferon-α/β over-amplification and auto-inflammation. Nature. 2014; 517(7532):89-93. PMC: 4303590. DOI: 10.1038/nature13801. View

Emsley P, Lohkamp B, Scott W, Cowtan K . Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 4):486-501. PMC: 2852313. DOI: 10.1107/S0907444910007493. View

Shi H, Yang K, Liu X, Liu X, Wei B, Shan Y . Positive regulation of interferon regulatory factor 3 activation by Herc5 via ISG15 modification. Mol Cell Biol. 2010; 30(10):2424-36. PMC: 2863703. DOI: 10.1128/MCB.01466-09. View

Zhao C, Beaudenon S, Kelley M, Waddell M, Yuan W, Schulman B . The UbcH8 ubiquitin E2 enzyme is also the E2 enzyme for ISG15, an IFN-alpha/beta-induced ubiquitin-like protein. Proc Natl Acad Sci U S A. 2004; 101(20):7578-82. PMC: 419648. DOI: 10.1073/pnas.0402528101. View

Molland K, Zhou Q, Mesecar A . A 2.2 Å resolution structure of the USP7 catalytic domain in a new space group elaborates upon structural rearrangements resulting from ubiquitin binding. Acta Crystallogr F Struct Biol Commun. 2014; 70(Pt 3):283-7. PMC: 3944686. DOI: 10.1107/S2053230X14002519. View

Ketscher L, Hannss R, Morales D, Basters A, Guerra S, Goldmann T . Selective inactivation of USP18 isopeptidase activity in vivo enhances ISG15 conjugation and viral resistance. Proc Natl Acad Sci U S A. 2015; 112(5):1577-82. PMC: 4321242. DOI: 10.1073/pnas.1412881112. View

10.

DCunha J, KNIGHT Jr E, Haas A, Truitt R, Borden E . Immunoregulatory properties of ISG15, an interferon-induced cytokine. Proc Natl Acad Sci U S A. 1996; 93(1):211-5. PMC: 40208. DOI: 10.1073/pnas.93.1.211. View

11.

Ernst A, Avvakumov G, Tong J, Fan Y, Zhao Y, Alberts P . A strategy for modulation of enzymes in the ubiquitin system. Science. 2013; 339(6119):590-5. PMC: 3815447. DOI: 10.1126/science.1230161. View

12.

Wallweber H, Tam C, Franke Y, Starovasnik M, Lupardus P . Structural basis of recognition of interferon-α receptor by tyrosine kinase 2. Nat Struct Mol Biol. 2014; 21(5):443-8. PMC: 4161281. DOI: 10.1038/nsmb.2807. View

13.

Ratia K, Kilianski A, Baez-Santos Y, Baker S, Mesecar A . Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease. PLoS Pathog. 2014; 10(5):e1004113. PMC: 4031219. DOI: 10.1371/journal.ppat.1004113. View

14.

McCoy A, Grosse-Kunstleve R, Adams P, Winn M, Storoni L, Read R . Phaser crystallographic software. J Appl Crystallogr. 2009; 40(Pt 4):658-674. PMC: 2483472. DOI: 10.1107/S0021889807021206. View

15.

Takeuchi T, Iwahara S, Saeki Y, Sasajima H, Yokosawa H . Link between the ubiquitin conjugation system and the ISG15 conjugation system: ISG15 conjugation to the UbcH6 ubiquitin E2 enzyme. J Biochem. 2006; 138(6):711-9. DOI: 10.1093/jb/mvi172. View

16.

El Oualid F, Merkx R, Ekkebus R, Hameed D, Smit J, de Jong A . Chemical synthesis of ubiquitin, ubiquitin-based probes, and diubiquitin. Angew Chem Int Ed Engl. 2010; 49(52):10149-53. PMC: 3021723. DOI: 10.1002/anie.201005995. View

17.

Wong J, Pung Y, Sze N, Chin K . HERC5 is an IFN-induced HECT-type E3 protein ligase that mediates type I IFN-induced ISGylation of protein targets. Proc Natl Acad Sci U S A. 2006; 103(28):10735-40. PMC: 1484417. DOI: 10.1073/pnas.0600397103. View

18.

Bieniossek C, Richmond T, Berger I . MultiBac: multigene baculovirus-based eukaryotic protein complex production. Curr Protoc Protein Sci. 2008; Chapter 5:Unit 5.20. DOI: 10.1002/0471140864.ps0520s51. View

19.

Bogunovic D, Byun M, Durfee L, Abhyankar A, Sanal O, Mansouri D . Mycobacterial disease and impaired IFN-γ immunity in humans with inherited ISG15 deficiency. Science. 2012; 337(6102):1684-8. PMC: 3507439. DOI: 10.1126/science.1224026. View

20.

Dastur A, Beaudenon S, Kelley M, Krug R, Huibregtse J . Herc5, an interferon-induced HECT E3 enzyme, is required for conjugation of ISG15 in human cells. J Biol Chem. 2006; 281(7):4334-8. DOI: 10.1074/jbc.M512830200. View