Crystal structure of the lasso peptide Sphingopyxin I (SpI)

Experimental Data Snapshot

  • Resolution: 0.85 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

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Structure and Mechanism of the Sphingopyxin I Lasso Peptide Isopeptidase.

Fage, C.D.Hegemann, J.D.Nebel, A.J.Steinbach, R.M.Zhu, S.Linne, U.Harms, K.Bange, G.Marahiel, M.A.

(2016) Angew Chem Int Ed Engl 55: 12717-12721

  • DOI: https://doi.org/10.1002/anie.201605232
  • Primary Citation of Related Structures:  
    5JQF, 5JRK, 5JRL

  • PubMed Abstract: 

    Lasso peptides are natural products that assume a unique lariat knot topology. Lasso peptide isopeptidases (IsoPs) eliminate this topology through isopeptide bond cleavage. To probe how these enzymes distinguish between substrates and hydrolyze only isopeptide bonds, we examined the structure and mechanism of a previously uncharacterized IsoP from the proteobacterium Sphingopyxis alaskensis RB2256 (SpI-IsoP). We demonstrate that SpI-IsoP efficiently and specifically linearizes the lasso peptide sphingopyxin I (SpI) and variants thereof. We also present crystal structures of SpI and SpI-IsoP, revealing a threaded topology for the former and a prolyl oligopeptidase (POP)-like fold for the latter. Subsequent structure-guided mutational analysis allowed us to propose roles for active-site residues. Our study sheds light on lasso peptide catabolism and expands the engineering potential of these fascinating molecules.

  • Organizational Affiliation

    Fachbereich Chemie, Fachgebiet Biochemie und LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032, Marburg, Germany.


Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sphingopyxin I
A, B
21Sphingopyxis alaskensis RB2256Mutation(s): 0 
Find proteins for A0A1D5B387 (Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256))
Explore A0A1D5B387 
Go to UniProtKB:  A0A1D5B387
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D5B387
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 0.85 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.24α = 90
b = 39.24β = 90
c = 31.41γ = 120
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermany--
LOEWE-Zentrum fuer Synthetische MikrobiologieGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2019-05-08
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2021-06-16
    Changes: Advisory, Atomic model, Derived calculations