4TVF | pdb_00004tvf

OxyB from Actinoplanes teichomyceticus

• PDB DOI: https://doi.org/10.2210/pdb4TVF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Actinoplanes teichomyceticus
• Expression System: Escherichia coli KRX
• Mutation(s): No 


• Deposited: 2014-06-26 Released: 2014-11-12 
• Deposition Author(s): Haslinger, K., Cryle, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.251 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Cytochrome P450 OxyBtei Catalyzes the First Phenolic Coupling Step in Teicoplanin Biosynthesis.

Haslinger, K., Maximowitsch, E., Brieke, C., Koch, A., Cryle, M.J.

(2014) Chembiochem 15: 2719-2728

• PubMed: 25358800 
• DOI: https://doi.org/10.1002/cbic.201402441
• Primary Citation Related Structures: 
  4TVF


• PubMed Abstract: 
  

  Bacterial cytochrome P450s form a remarkable clade of the P450 superfamily of oxidative hemoproteins, and are often involved in the biosynthesis of complex natural products. Those in a subgroup known as "Oxy enzymes" play a crucial role in the biosynthesis of glycopeptide antibiotics, including vancomycin and teicoplanin. The Oxy enzymes catalyze crosslinking of aromatic residues in the non-ribosomal antibiotic precursor peptide while it remains bound to the non-ribosomal peptide synthetase (NRPS); this crosslinking secures the three-dimensional structure of the glycopeptide, crucial for antibiotic activity. We have characterized OxyBtei , the first of the Oxy enzymes in teicoplanin biosynthesis. Our results reveal that OxyBtei possesses a structure similar to those of other Oxy proteins and is active in crosslinking NRPS-bound peptide substrates. However, OxyBtei displays a significantly altered activity spectrum against peptide substrates compared to its well-studied vancomycin homologue.

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Organizational Affiliation: 
• Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany).

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.27 kDa 
• Atom Count: 3,042 
• Modeled Residue Count: 352 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OxyB	A	431	Actinoplanes teichomyceticus	Mutation(s): 0  Gene Names: tcp20 EC: 1.14.14.1
UniProt
Find proteins for Q70AY8 (Actinoplanes teichomyceticus) Explore Q70AY8  Go to UniProtKB:  Q70AY8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.251 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.83	α = 90
b = 45.3	β = 102.46
c = 60.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Haslinger, K., Cryle, M.J.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2014-12-17
  Changes: Database references
• Version 1.2: 2014-12-24
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Refinement description