Crystal structure of RBBP9 in complex with phenylalanine

Experimental Data Snapshot

  • Resolution: 1.51 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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This is version 1.4 of the entry. See complete history


Mechanism-based traps enable protease and hydrolase substrate discovery.

Tang, S.Beattie, A.T.Kafkova, L.Petris, G.Huguenin-Dezot, N.Fiedler, M.Freeman, M.Chin, J.W.

(2022) Nature 602: 701-707

  • DOI: https://doi.org/10.1038/s41586-022-04414-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Hydrolase enzymes, including proteases, are encoded by 2-3% of the genes in the human genome and 14% of these enzymes are active drug targets 1 . However, the activities and substrate specificities of many proteases-especially those embedded in membranes-and other hydrolases remain unknown. Here we report a strategy for creating mechanism-based, light-activated protease and hydrolase substrate traps in complex mixtures and live mammalian cells. The traps capture substrates of hydrolases, which normally use a serine or cysteine nucleophile. Replacing the catalytic nucleophile with genetically encoded 2,3-diaminopropionic acid allows the first step reaction to form an acyl-enzyme intermediate in which a substrate fragment is covalently linked to the enzyme through a stable amide bond 2 ; this enables stringent purification and identification of substrates. We identify new substrates for proteases, including an intramembrane mammalian rhomboid protease RHBDL4 (refs.  3,4 ). We demonstrate that RHBDL4 can shed luminal fragments of endoplasmic reticulum-resident type I transmembrane proteins to the extracellular space, as well as promoting non-canonical secretion of endogenous soluble endoplasmic reticulum-resident chaperones. We also discover that the putative serine hydrolase retinoblastoma binding protein 9 (ref.  5 ) is an aminopeptidase with a preference for removing aromatic amino acids in human cells. Our results exemplify a powerful paradigm for identifying the substrates and activities of hydrolase enzymes.

  • Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK. stang@mrc-lmb.cam.ac.uk.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydrolase RBBP9
A, B
194Homo sapiensMutation(s): 0 
Gene Names: RBBP9BOGRBBP10
EC: 3
UniProt & NIH Common Fund Data Resources
Find proteins for O75884 (Homo sapiens)
Explore O75884 
Go to UniProtKB:  O75884
PHAROS:  O75884
GTEx:  ENSG00000089050 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75884
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.51 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.956α = 90
b = 130.127β = 115.24
c = 38.993γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105181009
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_A024_1008

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2022-03-02
    Changes: Database references
  • Version 1.3: 2022-03-09
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description