8RDO | pdb_00008rdo

Holomycin methyltransferase DtpM with SAH and XRD-271Me


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.220 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.203 (Depositor) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8RDO

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Isofunctional but Structurally Different Methyltransferases for Dithiolopyrrolone Diversification.

Su, L.Huber, E.M.Westphalen, M.Gellner, J.Bode, E.Kobel, T.Grun, P.Alanjary, M.M.Glatter, T.Cirnski, K.Muller, R.Schindler, D.Groll, M.Bode, H.B.

(2024) Angew Chem Int Ed Engl 63: e202410799-e202410799

  • DOI: https://doi.org/10.1002/anie.202410799
  • Primary Citation Related Structures: 
    8RDL, 8RDM, 8RDN, 8RDO

  • PubMed Abstract: 

    Dithiolopyrrolone (DTP) natural products are produced by several different bacteria and have potent antibacterial, antifungal and anticancer activities. While the amide of their DTP core can be methylated to fine-tune bioactivity, the enzyme responsible for the amide N-methylation has remained elusive in most taxa. Here, we identified the amide methyltransferase XrdM that is responsible for xenorhabdin (XRD) methylation in Xenorhabdus doucetiae but encoded outside of the XRD gene cluster. XrdM turned out to be isofunctional with the recently reported methyltransferase DtpM, that is involved in the biosynthesis of the DTP thiolutin, although its X-ray structure is unrelated to that of DtpM. To investigate the structural basis for ligand binding in both enzymes, we used X-ray crystallography, modeling, site-directed mutagenesis, and kinetic activity assays. Our study expands the limited knowledge of post-non-ribosomal peptide synthetase (NRPS) amide methylation in DTP biosynthesis and reveals an example of convergent evolution of two structurally completely different enzymes for the same reaction in different organisms.


  • Organizational Affiliation
    • Max Planck Institute for Terrestrial Microbiology, Natural products in organismic interactions, GERMANY.

Macromolecule Content 

  • Total Structure Weight: 39.46 kDa 
  • Atom Count: 2,782 
  • Modeled Residue Count: 340 
  • Deposited Residue Count: 352 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DtpM352Xenorhabdus doucetiae FRM16 = DSM 17909Mutation(s): 0 
Gene Names: J7S33_29485
UniProt
Find proteins for A0A8T8HXW2 (Saccharothrix algeriensis)
Explore A0A8T8HXW2 
Go to UniProtKB:  A0A8T8HXW2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8T8HXW2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
(Subject of Investigation/LOI)

Query on SAH



Download:Ideal Coordinates CCD File
B [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
YRD
(Subject of Investigation/LOI)

Query on YRD



Download:Ideal Coordinates CCD File
C [auth A]~{N}-(4-methyl-5-oxidanylidene-[1,2]dithiolo[4,3-b]pyrrol-6-yl)hexanamide
C12 H16 N2 O2 S2
ZXLPBBAXZZCKNU-UHFFFAOYSA-N
MLT

Query on MLT



Download:Ideal Coordinates CCD File
G [auth A]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.220 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.203 (Depositor) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.43α = 90
b = 53.43β = 90
c = 209.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1309-325871075

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references