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

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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