5JRK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.237 

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:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein
A, B
756Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256)Mutation(s): 0 
Find proteins for Q1GQ33 (Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256))
Go to UniProtKB:  Q1GQ33
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 111.105α = 90.00
b = 133.501β = 90.00
c = 169.070γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXmodel building
PHENIXrefinement
PHENIXphasing
Cootmodel building
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence