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NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway

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Journal of Structural and Functional Genomics

Abstract

For cell regulation, E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1) is involved in the transfer of ubiquitin-fold modifier 1 (Ufm1), a ubiquitin like protein which is activated by E1-like enzyme Uba5, to various target proteins. Thereby, Ufc1 participates in the very recently discovered Ufm1-Uba5-Ufc1 ubiquination pathway which is found in metazoan organisms. The structure of human Ufc1 was solved by using both NMR spectroscopy and X-ray crystallography. The complementary insights obtained with the two techniques provided a unique basis for understanding the function of Ufc1 at atomic resolution. The Ufc1 structure consists of the catalytic core domain conserved in all E2-like enzymes and an additional N-terminal helix. The active site Cys116, which forms a thio-ester bond with Ufm1, is located in a flexible loop that is highly solvent accessible. Based on the Ufc1 and Ufm1 NMR structures, a model could be derived for the Ufc1-Ufm1 complex in which the C-terminal Gly83 of Ufm1 may well form the expected thio-ester with Cys116, suggesting that Ufm1-Ufc1 functions as described for other E1–E2–E3 machineries. α-helix 1 of Ufc1 adopts different conformations in the crystal and in solution, suggesting that this helix plays a key role to mediate specificity.

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Abbreviations

ASU:

Asymmetric unit

E1:

Ubiquitin-activating enzyme

E2:

Ubiquitin-conjugating enzyme

E3:

Ubiquitin-protein ligase

NESG:

Northeast Structural Genomics Consortium

NMR:

Nuclear magnetic resonance

NSLF:

National synchrotron light source

PDB:

Protein data bank

SAD:

Single-wavelength anomalous diffraction

UBC:

Ubiquitin conjugating enzyme

UBL:

Ubiquitin-like (Ubl)

UFC1:

Ubiquitin-fold modifier conjugating enzyme 1

UFM1:

Ubiquitin-fold modifier 1

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Acknowledgments

This work was supported by the Protein Structure Initiative of the National Institutes of Health (U54-GM074958) and the National Science Foundation (MCB 0416899 to T.S.). The authors thank Dr. Goldsmith-Fischman for helpful discussions on the structural biology of Ufc1.

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Correspondence to Thomas Szyperski.

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Gaohua Liu and Farhad Forouhar have made equal contributions to this work and they both should be considered as first authors.

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Liu, G., Forouhar, F., Eletsky, A. et al. NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway. J Struct Funct Genomics 10, 127–136 (2009). https://doi.org/10.1007/s10969-008-9054-7

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