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Structural and thermodynamic comparison of the catalytic domain of AMSH and AMSH-LP: nearly identical fold but different stability.

Davies CW, Paul LN, Kim MI, Das C
J Mol Biol 413 416-29 (2011)
Cited: 42 times
EuropePMC logo PMID: 21888914

Abstract

AMSH plays a critical role in the ESCRT (endosomal sorting complexes required for transport) machinery, which facilitates the down-regulation and degradation of cell-surface receptors. It displays a high level of specificity toward cleavage of Lys63-linked polyubiquitin chains, the structural basis of which has been understood recently through the crystal structure of a highly related, but ESCRT-independent, protein AMSH-LP (AMSH-like protein). We have determined the X-ray structure of two constructs representing the catalytic domain of AMSH: AMSH244, the JAMM (JAB1/MPN/MOV34)-domain-containing polypeptide segment from residues 244 to 424, and AMSH219(E280A), an active-site mutant, Glu280 to Ala, of the segment from 219 to 424. In addition to confirming the expected zinc coordination in the protein, the structures reveal that the catalytic domains of AMSH and AMSH-LP are nearly identical; however, guanidine-hydrochloride-induced unfolding studies show that the catalytic domain of AMSH is thermodynamically less stable than that of AMSH-LP, indicating that the former is perhaps structurally more plastic. Much to our surprise, in the AMSH219(E280A) structure, the catalytic zinc was still held in place, by the compensatory effect of an aspartate from a nearby loop moving into a position where it could coordinate with the zinc, once again suggesting the plasticity of AMSH. Additionally, a model of AMSH244 bound to Lys63-linked diubiquitin reveals a type of interface for the distal ubiquitin significantly different from that seen in AMSH-LP. Altogether, we believe that our data provide important insight into the structural difference between the two proteins that may translate into the difference in their biological function.

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  1. Early‑onset epilepsy and microcephaly‑capillary malformation syndrome caused by a novel STAMBP mutation in a Chinese boy. Wu F, Dai Y, Wang J, Cheng M, Wang Y, Li X, Yuan P, Liao S, Jiang L, Chen J, Yan L, Zhong M. Mol Med Rep 20 5145-5151 (2019)

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  3. Structural and thermodynamic comparison of the catalytic domain of AMSH and AMSH-LP: nearly identical fold but different stability. Davies CW, Paul LN, Kim MI, Das C. J Mol Biol 413 416-429 (2011)
  4. Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. Macchiagodena M, Pagliai M, Andreini C, Rosato A, Procacci P. ACS Omega 5 15301-15310 (2020)
  5. Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins. Dürr SL, Levy A, Rothlisberger U. Nat Commun 14 2713 (2023)
  6. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)


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  1. Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Worden EJ, Padovani C, Martin A. Nat Struct Mol Biol 21 220-227 (2014)
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  4. Lysine 63-linked polyubiquitination is required for EGF receptor degradation. Huang F, Zeng X, Kim W, Balasubramani M, Fortian A, Gygi SP, Yates NA, Sorkin A. Proc Natl Acad Sci U S A 110 15722-15727 (2013)
  5. Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome. McDonell LM, Mirzaa GM, Alcantara D, Schwartzentruber J, Carter MT, Lee LJ, Clericuzio CL, Graham JM, Morris-Rosendahl DJ, Polster T, Acsadi G, Townshend S, Williams S, Halbert A, Isidor B, David A, Smyser CD, Paciorkowski AR, Willing M, Woulfe J, Das S, Beaulieu CL, Marcadier J, FORGE Canada Consortium, Geraghty MT, Frey BJ, Majewski J, Bulman DE, Dobyns WB, O'Driscoll M, Boycott KM. Nat Genet 45 556-562 (2013)
  6. Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4. Bodnar NO, Kim KH, Ji Z, Wales TE, Svetlov V, Nudler E, Engen JR, Walz T, Rapoport TA. Nat Struct Mol Biol 25 616-622 (2018)
  7. Discovery of an Inhibitor of the Proteasome Subunit Rpn11. Perez C, Li J, Parlati F, Rouffet M, Ma Y, Mackinnon AL, Chou TF, Deshaies RJ, Cohen SM. J Med Chem 60 1343-1361 (2017)
  8. Insights into the mechanism of deubiquitination by JAMM deubiquitinases from cocrystal structures of the enzyme with the substrate and product. Shrestha RK, Ronau JA, Davies CW, Guenette RG, Strieter ER, Paul LN, Das C. Biochemistry 53 3199-3217 (2014)
  9. Targeting the deubiquitinase STAMBP inhibits NALP7 inflammasome activity. Bednash JS, Weathington N, Londino J, Rojas M, Gulick DL, Fort R, Han S, McKelvey AC, Chen BB, Mallampalli RK. Nat Commun 8 15203 (2017)
  10. Archaeal JAB1/MPN/MOV34 metalloenzyme (HvJAMM1) cleaves ubiquitin-like small archaeal modifier proteins (SAMPs) from protein-conjugates. Hepowit NL, Uthandi S, Miranda HV, Toniutti M, Prunetti L, Olivarez O, De Vera IM, Fanucci GE, Chen S, Maupin-Furlow JA. Mol Microbiol 86 971-987 (2012)
  11. Mechanism of recruitment and activation of the endosome-associated deubiquitinase AMSH. Davies CW, Paul LN, Das C. Biochemistry 52 7818-7829 (2013)
  12. The crystal structure of the MPN domain from the COP9 signalosome subunit CSN6. Zhang H, Zhang H, Gao ZQ, Wang WJ, Liu GF, Shtykova EV, Xu JH, Li LF, Su XD, Dong YH. FEBS Lett 586 1147-1153 (2012)
  13. Validation and correction of Zn-CysxHisy complexes. Touw WG, van Beusekom B, Evers JM, Vriend G, Joosten RP. Acta Crystallogr D Struct Biol 72 1110-1118 (2016)
  14. Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities. Pham GH, Rana AS, Korkmaz EN, Trang VH, Cui Q, Strieter ER. Protein Sci 25 456-471 (2016)
  15. Divergence in Ubiquitin Interaction and Catalysis among the Ubiquitin-Specific Protease Family Deubiquitinating Enzymes. Tencer AH, Liang Q, Zhuang Z. Biochemistry 55 4708-4719 (2016)
  16. Dynamics of an Active-Site Flap Contributes to Catalysis in a JAMM Family Metallo Deubiquitinase. Bueno AN, Shrestha RK, Ronau JA, Babar A, Sheedlo MJ, Fuchs JE, Paul LN, Das C. Biochemistry 54 6038-6051 (2015)
  17. High-throughput compatible fluorescence resonance energy transfer-based assay to identify small molecule inhibitors of AMSH deubiquitinase activity. Arnst JL, Davies CW, Raja SM, Das C, Natarajan A. Anal Biochem 440 71-77 (2013)
  18. The Vps27/Hrs/STAM (VHS) Domain of the Signal-transducing Adaptor Molecule (STAM) Directs Associated Molecule with the SH3 Domain of STAM (AMSH) Specificity to Longer Ubiquitin Chains and Dictates the Position of Cleavage. Baiady N, Padala P, Mashahreh B, Cohen-Kfir E, Todd EA, Du Pont KE, Berndsen CE, Wiener R. J Biol Chem 291 2033-2042 (2016)
  19. Ubiquitin and its relatives as wizards of the endolysosomal system. Berlin I, Sapmaz A, Stévenin V, Neefjes J. J Cell Sci 136 jcs260101 (2023)
  20. DRJAMM Is Involved in the Oxidative Resistance in Deinococcus radiodurans. Cai J, Pan C, Zhao Y, Xu H, Tian B, Wang L, Hua Y. Front Microbiol 12 756867 (2021)
  21. Crystal structure of the Thr316Ala mutant of a yeast JAMM deubiquitinase: implication of active-site loop dynamics in catalysis. Shrestha R, Das C. Acta Crystallogr F Struct Biol Commun 77 163-170 (2021)
  22. Linkage-specific ubiquitin binding interfaces modulate the activity of the chlamydial deubiquitinase Cdu1 towards poly-ubiquitin substrates. Schlötzer J, Schmalix A, Hügelschäffer S, Rieger D, Sauer F, Tully MD, Rudel T, Wiesner S, Kisker C. PLoS Pathog 20 e1012630 (2024)


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