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Crystal structure of the complex between prokaryotic ubiquitin-like protein and its ligase PafA.

Barandun J, Delley CL, Ban N, Weber-Ban E
J Am Chem Soc 135 6794-7 (2013)
Cited: 21 times
EuropePMC logo PMID: 23601177

Abstract

Prokaryotic ubiquitin-like protein (Pup) is covalently attached to target proteins by the ligase PafA, tagging substrates for proteasomal degradation. The crystal structure of Pup in complex with PafA, reported here, reveals that a long groove wrapping around the enzyme serves as a docking site for Pup. Upon binding, the C-terminal region of the intrinsically disordered Pup becomes ordered to form two helices connected by a linker, positioning the C-terminal glutamate in the active site of PafA.

Reviews - 4bjr mentioned but not cited (1)

  1. Prokaryotic ubiquitin-like protein modification. Maupin-Furlow JA. Annu Rev Microbiol 68 155-175 (2014)

Articles - 4bjr mentioned but not cited (5)

  1. Inter- and intramolecular regulation of protein depupylation in Mycobacterium smegmatis. Hecht N, Becher M, Korman M, Vishkautzan M, Gur E. FEBS J 287 4389-4400 (2020)
  2. Exploring Protein Space: From Hydrolase to Ligase by Substitution. Hecht N, Monteil CL, Perrière G, Vishkautzan M, Gur E. Mol Biol Evol 38 761-776 (2021)
  3. Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis. Jiang HW, Czajkowsky DM, Wang T, Wang XD, Wang JB, Zhang HN, Liu CX, Wu FL, He X, Xu ZW, Chen H, Guo SJ, Li Y, Bi LJ, Deng JY, Xie J, Pei JF, Zhang XE, Tao SC. EBioMedicine 30 225-236 (2018)
  4. Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation. Cui H, Müller AU, Leibundgut M, Tian J, Ban N, Weber-Ban E. Nat Commun 12 6635 (2021)
  5. Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA. Block MF, Delley CL, Keller LML, Stuehlinger TT, Weber-Ban E. Nat Commun 14 5266 (2023)


Reviews citing this publication (6)

  1. Bacterial Proteasomes. Jastrab JB, Darwin KH. Annu Rev Microbiol 69 109-127 (2015)
  2. Bacterial Proteasomes: Mechanistic and Functional Insights. Becker SH, Darwin KH. Microbiol Mol Biol Rev 81 e00036-16 (2017)
  3. Prokaryotic Ubiquitin-Like Protein and Its Ligase/Deligase Enyzmes. Delley CL, Müller AU, Ziemski M, Weber-Ban E. J Mol Biol 429 3486-3499 (2017)
  4. Biology and Biochemistry of Bacterial Proteasomes. Becker SH, Li H, Li H, Heran Darwin K. Subcell Biochem 93 339-358 (2019)
  5. Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways. von Rosen T, Keller LM, Weber-Ban E. Front Mol Biosci 8 685757 (2021)
  6. Digested disorder: Quarterly intrinsic disorder digest (April-May-June, 2013). DeForte S, Reddy KD, Uversky VN. Intrinsically Disord Proteins 1 e27454 (2013)

Articles citing this publication (9)

  1. Bacterial proteasome activator bpa (rv3780) is a novel ring-shaped interactor of the mycobacterial proteasome. Delley CL, Laederach J, Ziemski M, Bolten M, Boehringer D, Weber-Ban E. PLoS One 9 e114348 (2014)
  2. Involvement of a eukaryotic-like ubiquitin-related modifier in the proteasome pathway of the archaeon Sulfolobus acidocaldarius. Anjum RS, Bray SM, Blackwood JK, Kilkenny ML, Coelho MA, Foster BM, Li S, Howard JA, Pellegrini L, Albers SV, Deery MJ, Robinson NP. Nat Commun 6 8163 (2015)
  3. Posttranslational regulation of coordinated enzyme activities in the Pup-proteasome system. Elharar Y, Roth Z, Hecht N, Rotkopf R, Khalaila I, Gur E. Proc Natl Acad Sci U S A 113 E1605-14 (2016)
  4. Depupylase Dop Requires Inorganic Phosphate in the Active Site for Catalysis. Bolten M, Vahlensieck C, Lipp C, Leibundgut M, Ban N, Weber-Ban E. J Biol Chem 292 4044-4053 (2017)
  5. Prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins. Barandun J, Damberger FF, Delley CL, Laederach J, Allain FH, Weber-Ban E, Weber-Ban E. BMC Struct Biol 17 1 (2017)
  6. The Mechanism of Mycobacterium smegmatis PafA Self-Pupylation. Chen X, Li C, Wang L, Liu Y, Li C, Zhang J. PLoS One 11 e0151021 (2016)
  7. An Extended Loop of the Pup Ligase, PafA, Mediates Interaction with Protein Targets. Regev O, Korman M, Hecht N, Roth Z, Forer N, Zarivach R, Gur E. J Mol Biol 428 4143-4153 (2016)
  8. Structural basis of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa-proteasome complex. Kavalchuk M, Jomaa A, Jomaa A, Müller AU, Weber-Ban E. Nat Commun 13 276 (2022)
  9. Pupylated proteins are subject to broad proteasomal degradation specificity and differential depupylation. Laederach J, Cui H, Weber-Ban E. PLoS One 14 e0215439 (2019)


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