8BYK | pdb_00008byk

The structure of MadC from Clostridium maddingley reveals new insights into class I lanthipeptide cyclases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.220 (Depositor), 0.171 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.126 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

The structure of MadC from Clostridium maddingley reveals new insights into class I lanthipeptide cyclases.

Knospe, C.V.Kamel, M.Spitz, O.Hoeppner, A.Galle, S.Reiners, J.Kedrov, A.Smits, S.H.J.Schmitt, L.

(2022) Front Microbiol 13: 1057217-1057217

  • DOI: https://doi.org/10.3389/fmicb.2022.1057217
  • Primary Citation Related Structures: 
    8BYK

  • PubMed Abstract: 

    The rapid emergence of microbial multi-resistance against antibiotics has led to intense search for alternatives. One of these alternatives are ribosomally synthesized and post-translationally modified peptides (RiPPs), especially lantibiotics. They are active in a low nanomolar range and their high stability is due to the presence of characteristic (methyl-) lanthionine rings, which makes them promising candidates as bacteriocides. However, innate resistance against lantibiotics exists in nature, emphasizing the need for artificial or tailor-made lantibiotics. Obviously, such an approach requires an in-depth mechanistic understanding of the modification enzymes, which catalyze the formation of (methyl-)lanthionine rings. Here, we determined the structure of a class I cyclase (MadC), involved in the modification of maddinglicin (MadA) via X-ray crystallography at a resolution of 1.7 Å, revealing new insights about the structural composition of the catalytical site. These structural features and substrate binding were analyzed by mutational analyses of the leader peptide as well as of the cyclase, shedding light into the mode of action of MadC.


  • Organizational Affiliation
    • Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.

Macromolecule Content 

  • Total Structure Weight: 51.38 kDa 
  • Atom Count: 3,886 
  • Modeled Residue Count: 437 
  • Deposited Residue Count: 449 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lanthionine synthetase C-like protein449ClostridiumMutation(s): 0 
Gene Names: A370_05564
UniProt
Find proteins for A0ACD6B9R6 (Clostridium sp. Maddingley MBC34-26)
Explore A0ACD6B9R6 
Go to UniProtKB:  A0ACD6B9R6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B9R6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD

Query on MPD



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
H [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.220 (Depositor), 0.171 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.126 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.14α = 90
b = 66.119β = 90
c = 117.258γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySchm1279/13-1
German Research Foundation (DFG)Germany417919780

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection