6M9S | pdb_00006m9s

Crystal structure of SeMet SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.189 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6M9S

This is version 1.4 of the entry. See complete history

Literature

An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin.

Ng, T.L.Rohac, R.Mitchell, A.J.Boal, A.K.Balskus, E.P.

(2019) Nature 566: 94-99

  • DOI: https://doi.org/10.1038/s41586-019-0894-z
  • Primary Citation Related Structures: 
    6M9R, 6M9S

  • PubMed Abstract: 

    Small molecules containing the N-nitroso group, such as the bacterial natural product streptozotocin, are prominent carcinogens 1,2 and important cancer chemotherapeutics 3,4 . Despite the considerable importance of this functional group to human health, enzymes dedicated to the assembly of the N-nitroso unit have not been identified. Here we show that SznF, a metalloenzyme from the biosynthesis of streptozotocin, catalyses an oxidative rearrangement of the guanidine group of N ω -methyl-L-arginine to generate an N-nitrosourea product. Structural characterization and mutagenesis of SznF reveal two separate active sites that promote distinct steps in this transformation using different iron-containing metallocofactors. This biosynthetic reaction, which has little precedent in enzymology or organic synthesis, expands the catalytic capabilities of non-haem-iron-dependent enzymes to include N-N bond formation. We find that biosynthetic gene clusters that encode SznF homologues are widely distributed among bacteria-including environmental organisms, plant symbionts and human pathogens-which suggests an unexpectedly diverse and uncharacterized microbial reservoir of bioactive N-nitroso metabolites.


  • Organizational Affiliation
    • Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 226.25 kDa 
  • Atom Count: 16,254 
  • Modeled Residue Count: 1,823 
  • Deposited Residue Count: 1,952 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SznF
A, B, C, D
488Streptomyces achromogenes subsp. streptozoticusMutation(s): 0 
Gene Names: sznf
EC: 1

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A],
N [auth B],
R [auth C],
W [auth D],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
M [auth B],
Q [auth C],
V [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
J [auth A],
S [auth C]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
K [auth B]
L [auth B]
O [auth C]
E [auth A],
F [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
T [auth D],
U [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.189 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.51α = 90
b = 109.46β = 90
c = 365.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
HKL2Mapphasing
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States119707

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-13
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary