3GYR

Structure of Phenoxazinone synthase from Streptomyces antibioticus reveals a new type 2 copper center.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Phenoxazinone Synthase from Streptomyces Antibioticus Reveals a New Type 2 Copper Center.

Smith, A.W.Camara-Artigas, A.Wang, M.Allen, J.P.Francisco, W.A.

(2006) Biochemistry 45: 4378

  • DOI: 10.1021/bi0525526
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The multicopper oxidase phenoxazinone synthase (PHS) catalyzes the penultimate step in the biosynthesis of the antibiotic actinomycin D by Streptomyces antibioticus. PHS exists in two oligomeric forms: a dimeric form and a hexameric form, with older ...

    The multicopper oxidase phenoxazinone synthase (PHS) catalyzes the penultimate step in the biosynthesis of the antibiotic actinomycin D by Streptomyces antibioticus. PHS exists in two oligomeric forms: a dimeric form and a hexameric form, with older actinomycin-producing cultures containing predominately the hexameric form. The structure of hexameric PHS has been determined using X-ray diffraction to a resolution limit of 2.30 A and is found to contain several unexpected and distinctive features. The structure forms a hexameric ring that is centered on a pseudo 6-fold axis and has an outer diameter of 185 A with a large central cavity that has a diameter of 50 A. This hexameric structure is stabilized by a long loop connecting two domains; bound to this long loop is a fifth copper atom that is present as a type 2 copper. This copper atom is not present in any other multicopper oxidase, and its presence appears to stabilize the hexameric structure.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Arizona State University, Tempe Arizona 85287-1604, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenoxazinone synthase
A, B, C, D, E, F, G, H, I, J, K, L
612Streptomyces antibioticusMutation(s): 1 
Gene Names: phsA
EC: 1.10.3.4
Find proteins for Q53692 (Streptomyces antibioticus)
Go to UniProtKB:  Q53692
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
C2O
Query on C2O

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
CU-O-CU LINKAGE
Cu2 O
BERDEBHAJNAUOM-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.165 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 109.494α = 117.04
b = 163.456β = 95.74
c = 164.352γ = 107.23
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
CCP4data scaling
REFMACrefinement
MOSFLMdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Derived calculations, Refinement description, Version format compliance
  • Version 1.2: 2018-04-04
    Type: Data collection
  • Version 1.3: 2019-07-24
    Type: Data collection, Refinement description