5V1S

Crystal structure of Streptococcus suis SuiB bound to S-adenosylmethionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.492 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition.

Davis, K.M.Schramma, K.R.Hansen, W.A.Bacik, J.P.Khare, S.D.Seyedsayamdost, M.R.Ando, N.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 10420-10425

  • DOI: 10.1073/pnas.1703663114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader s ...

    Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. Here, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine-tryptophan cross-link, which is installed by the radical S-adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon-carbon cross-link in the streptide family of natural products.


    Organizational Affiliation

    Department of Chemistry, Princeton University, Princeton, NJ 08544.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Radical SAM
A, B
459Streptococcus suisMutation(s): 0 
Gene Names: kwcM
Find proteins for A0A0Z8EWX1 (Streptococcus suis)
Go to UniProtKB:  A0A0Z8EWX1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.492 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.787α = 90.00
b = 85.473β = 90.00
c = 109.864γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references
  • Version 1.2: 2017-10-11
    Type: Database references