3GYR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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:  
    3GYR

  • 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 actinomycin-producing cultures containing predominately the hexameric form ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenoxazinone synthase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
612Streptomyces antibioticusMutation(s): 1 
Gene Names: phsA
EC: 1 (PDB Primary Data), 1.10.3.4 (UniProt)
Find proteins for Q53692 (Streptomyces antibioticus)
Explore Q53692 
Go to UniProtKB:  Q53692
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2O
Query on C2O

Download Ideal Coordinates CCD File 
DB [auth I] , EA [auth D] , IB [auth J] , JA [auth E] , NB [auth K] , OA [auth F] , P [auth A] , SB [auth L] , 
DB [auth I],  EA [auth D],  IB [auth J],  JA [auth E],  NB [auth K],  OA [auth F],  P [auth A],  SB [auth L],  TA [auth G],  U [auth B],  YA [auth H],  Z [auth C]
CU-O-CU LINKAGE
Cu2 O
BERDEBHAJNAUOM-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C] , EB [auth I] , FA [auth D] , JB [auth J] , KA [auth E] , OB [auth K] , PA [auth F] , Q [auth A] , 
AA [auth C],  EB [auth I],  FA [auth D],  JB [auth J],  KA [auth E],  OB [auth K],  PA [auth F],  Q [auth A],  TB [auth L],  UA [auth G],  V [auth B],  ZA [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
AB [auth I] , BA [auth D] , BB [auth I] , CA [auth D] , CB [auth I] , DA [auth D] , FB [auth J] , GA [auth E] , 
AB [auth I],  BA [auth D],  BB [auth I],  CA [auth D],  CB [auth I],  DA [auth D],  FB [auth J],  GA [auth E],  GB [auth J],  HA [auth E],  HB [auth J],  IA [auth E],  KB [auth K],  LA [auth F],  LB [auth K],  M [auth A],  MA [auth F],  MB [auth K],  N [auth A],  NA [auth F],  O [auth A],  PB [auth L],  QA [auth G],  QB [auth L],  R [auth B],  RA [auth G],  RB [auth L],  S [auth B],  SA [auth G],  T [auth B],  VA [auth H],  W [auth C],  WA [auth H],  X [auth C],  XA [auth H],  Y [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • 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
REFMACrefinement
CNSrefinement
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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