5JRL

Crystal Structure of the Sphingopyxin I Lasso Peptide Isopeptidase SpI-IsoP (Native)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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) ...

    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. marahiel@staff.uni-marburg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like proteinA, B, C, D756Sphingopyxis alaskensis RB2256Mutation(s): 0 
Gene Names: Sala_2532
UniProt
Find proteins for Q1GQ33 (Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256))
Explore Q1GQ33 
Go to UniProtKB:  Q1GQ33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1GQ33
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.466α = 90
b = 136.586β = 97.62
c = 110.777γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building

Structure Validation

View Full Validation Report



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: 2016-11-09
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence