5HH3 | pdb_00005hh3

OxyA from Actinoplanes teichomyceticus

• PDB DOI: https://doi.org/10.2210/pdb5HH3/pdb

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


• Deposited: 2016-01-09 Released: 2016-02-10 
• Deposition Author(s): Haslinger, K., Cryle, M.J.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.229 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Structure of OxyAtei : completing our picture of the glycopeptide antibiotic producing Cytochrome P450 cascade.

Haslinger, K., Cryle, M.J.

(2016) FEBS Lett 590: 571-581

• PubMed: 26820384 
• DOI: https://doi.org/10.1002/1873-3468.12081
• Primary Citation Related Structures: 
  5HH3


• PubMed Abstract: 
  

  Cyclization of glycopeptide antibiotic precursors occurs in either three or four steps catalyzed by Cytochrome P450 enzymes. Three of these enzymes have been structurally characterized to date with the second enzyme along the pathway, OxyA, escaping structural analysis. We are now able to present the structure of OxyAtei involved in teicoplanin biosynthesis - the same enzyme recently shown to be the first active OxyA homolog. In spite of the hydrophobic character of the teicoplanin precursor, the polar active site of OxyAtei and its affinity for certain azole inhibitors hint at its preference for substrates with polar decorations.

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Organizational Affiliation: 
• Max Planck Institute for Medical Research, Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 91.19 kDa 
• Atom Count: 6,471 
• Modeled Residue Count: 774 
• Deposited Residue Count: 794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OxyA protein	A, B [auth C]	397	Actinoplanes teichomyceticus	Mutation(s): 0  Gene Names: tcp18
UniProt
Find proteins for Q6ZZI8 (Actinoplanes teichomyceticus) Explore Q6ZZI8  Go to UniProtKB:  Q6ZZI8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], G [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	D [auth A], E [auth A], H [auth C], I [auth C], J [auth C], K [auth C], L [auth C], M [auth C], N [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth A], O [auth C], P [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.229 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.49	α = 90
b = 103.06	β = 90
c = 152.97	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Haslinger, K., Cryle, M.J.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	CR 392/1-1

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-03-02
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description