6M7L

Complex of OxyA with the X-domain from GPA biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Kistamicin biosynthesis reveals the biosynthetic requirements for production of highly crosslinked glycopeptide antibiotics.

Greule, A.Izore, T.Iftime, D.Tailhades, J.Schoppet, M.Zhao, Y.Peschke, M.Ahmed, I.Kulik, A.Adamek, M.Goode, R.J.A.Schittenhelm, R.B.Kaczmarski, J.A.Jackson, C.J.Ziemert, N.Krenske, E.H.De Voss, J.J.Stegmann, E.Cryle, M.J.

(2019) Nat Commun 10: 2613-2613

  • DOI: https://doi.org/10.1038/s41467-019-10384-w
  • Primary Citation of Related Structures:  
    6M7L

  • PubMed Abstract: 

    Kistamicin is a divergent member of the glycopeptide antibiotics, a structurally complex class of important, clinically relevant antibiotics often used as the last resort against resistant bacteria. The extensively crosslinked structure of these antibiotics that is essential for their activity makes their chemical synthesis highly challenging and limits their production to bacterial fermentation. Kistamicin contains three crosslinks, including an unusual 15-membered A-O-B ring, despite the presence of only two Cytochrome P450 Oxy enzymes thought to catalyse formation of such crosslinks within the biosynthetic gene cluster. In this study, we characterise the kistamicin cyclisation pathway, showing that the two Oxy enzymes are responsible for these crosslinks within kistamicin and that they function through interactions with the X-domain, unique to glycopeptide antibiotic biosynthesis. We also show that the kistamicin OxyC enzyme is a promiscuous biocatalyst, able to install multiple crosslinks into peptides containing phenolic amino acids.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative non-ribosomal peptide synthetaseA [auth B]486[Actinomadura] parvosata subsp. kistnaeMutation(s): 0 
Gene Names: KIS93_04814
UniProt
Find proteins for A0A2P9IBG7 (Actinomadura parvosata subsp. kistnae)
Explore A0A2P9IBG7 
Go to UniProtKB:  A0A2P9IBG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P9IBG7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative cytochrome P450 hydroxylaseB [auth A]404[Actinomadura] parvosata subsp. kistnaeMutation(s): 0 
Gene Names: KIS93_04812
UniProt
Find proteins for A0A2P9IBF7 (Actinomadura parvosata subsp. kistnae)
Explore A0A2P9IBF7 
Go to UniProtKB:  A0A2P9IBF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P9IBF7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.834α = 90
b = 87.344β = 95.769
c = 95.955γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1140619
Australian Research Council (ARC)AustraliaDP170102220
German Research Foundation (DFG)GermanyCR 392/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Structure summary
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description