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Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1

Nature Structural & Molecular Biology volume 18, pages 604–613 (2011)Cite this article

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Abstract

ERAP1 trims antigen precursors to fit into MHC class I proteins. To fulfill this function, ERAP1 has unique substrate preferences, trimming long peptides but sparing shorter ones. To identify the structural basis for ERAP1's unusual properties, we determined the X-ray crystal structure of human ERAP1 bound to bestatin. The structure reveals an open conformation with a large interior compartment. An extended groove originating from the enzyme's catalytic center can accommodate long peptides and has features that explain ERAP1's broad specificity for antigenic peptide precursors. Structural and biochemical analyses suggest a mechanism for ERAP1's length-dependent trimming activity, whereby binding of long rather than short substrates induces a conformational change with reorientation of a key catalytic residue toward the active site. ERAP1's unique structural elements suggest how a generic aminopeptidase structure has been adapted for the specialized function of trimming antigenic precursors.

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Figure 1: ERAP1 structure and domain arrangement.
Figure 2: ERAP1 active site.
Figure 3: Open and closed conformations of ERAP1.
Figure 4: Length-dependent peptide cleavage and allosteric activation by ERAP1.
Figure 5: Kinetic analysis.
Figure 6: Non-hydrolyzable peptide activates L-AMC hydrolysis but inhibits full-length peptide hydrolysis.
Figure 7: Model for ERAP1 length-dependent cleavage activity.
Figure 8: Ankylosing spondylitis–associated mutations mapped on the surface of ERAP1.

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Change history

  • 24 April 2011

    In the version of this article initially published online, nucleotide should have read peptide in a number of places. The error has been corrected for all versions of this article.

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Acknowledgements

We thank E. Livaniou and P. Klimentzou (National Centre for Scientific Research 'Demokritos') for assistance with chemical synthesis of the LMe peptide, L. Lee for cell culture, L. Lu for assistance with baculovirus, protein expression and purification, D. Panne, Z. Zavala-Ruiz and E. Schreiter for help with cryocrystallography, and H. Robinson, A. Heroux and V. Stojanoff for assistance with data collection. Data for this study were measured at beamlines X6, X25 and X29 of the National Synchrotron Light Source. These beamlines are supported by the Offices of Biological and Environmental Research and of Basic Energy Sciences of the US Department of Energy, and by the National Center for Research Resources of the National Institutes of Health. Resources of the University of Massachusetts Medical School Mass Spectrometry Facility and Diabetes and Endocrine Research Center were used. Funding for this work was provided by the Sixth Framework Programme of the European Union (Marie Curie International Reintegration grant 017157 to E.S.) and the National Institutes of Health grants AI-38996 (L.J.S.). I.E. acknowledges financial support from NCSR Demokritos graduate fellowship program. L.J.S. and K.L.R. are members of the University of Massachusetts Diabetes and Endocrinology Research Center (DK32520).

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Author notes

  1. Shih-Chung Chang & Ian A York

    Present address: Present addresses: Institute of Microbiology and Biochemistry, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan. (S.C.C.); Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA. (I.A.Y.).,

Authors and Affiliations

  1. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    Tina T Nguyen & Lawrence J Stern

  2. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts

    Shih-Chung Chang & Alfred L Goldberg

  3. National Centre for Scientific Research 'Demokritos', Aghia Paraskevi, Greece

    Irini Evnouchidou, Christos Zikos & Efstratios Stratikos

  4. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA

    Ian A York

  5. Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA

    Kenneth L Rock & Lawrence J Stern

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  1. Tina T Nguyen
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Contributions

T.T.N. determined the crystal structure, designed and conducted enzymatic studies, interpreted results and helped write the paper, S.-C.C. expressed ERAP1 in insect cells and designed and conducted peptide trimming and allosteric activation experiments, I.E. designed and conducted peptide trimming and allosteric activation and inhibition experiments and interpreted results, I.A.Y. interpreted data and helped write the paper, C.Z. synthesized the LMe peptide, K.L.R. and A.L.G. designed experiments, interpreted data and helped write the paper, and E.S. and L.J.S. designed and conducted experiments, interpreted data and helped write the paper.

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Correspondence to Lawrence J Stern.

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Nguyen, T., Chang, SC., Evnouchidou, I. et al. Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1. Nat Struct Mol Biol 18, 604–613 (2011). https://doi.org/10.1038/nsmb.2021

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