6M7L | pdb_00006m7l

Complex of OxyA with the X-domain from GPA biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb6M7L/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): [Actinomadura] parvosata subsp. kistnae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-20 Released: 2019-05-22 
• Deposition Author(s): Greule, A., Izore, T., Tailhades, J., Peschke, M., Schoppet, M., Ahmed, I., Kulik, A., Adamek, M., Ziemert, N., De Voss, J., Stegmann, E., Cryle, M.J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC), German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.264 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

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

• PubMed: 31197182 
• DOI: https://doi.org/10.1038/s41467-019-10384-w
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
EMBL Australia, Monash University, Clayton, VIC, 3800, Australia.
Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.
Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia.
Monash Biomedical Proteomics Facility, Monash University, Clayton, VIC, 3800, Australia.
Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia.
Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany. [e-mail].
German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076, Tübingen, Germany. [e-mail].
Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. [e-mail].
EMBL Australia, Monash University, Clayton, VIC, 3800, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.16 kDa 
• Atom Count: 6,233 
• Modeled Residue Count: 792 
• Deposited Residue Count: 890 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative non-ribosomal peptide synthetase	A [auth B]	486	[Actinomadura] parvosata subsp. kistnae	Mutation(s): 0  Gene Names: KIS93_04814

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cytochrome P450 hydroxylase	B [auth A]	404	[Actinomadura] parvosata subsp. kistnae	Mutation(s): 0  Gene Names: KIS93_04812

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	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 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.834	α = 90
b = 87.344	β = 95.769
c = 95.955	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Greule, A., Izore, T., Tailhades, J., Peschke, M., Schoppet, M., Ahmed, I., Kulik, A., Adamek, M., Ziemert, N., De Voss, J., Stegmann, E., Cryle, M.J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1140619
Australian Research Council (ARC)	Australia	DP170102220
German Research Foundation (DFG)	Germany	CR 392/1-1

Revision History  

• 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