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 1.4 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenoxazinone synthase
A, B, C, D, E, F, G, H, I, J, K, L
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)
UniProt
Find proteins for Q53692 (Streptomyces antibioticus)
Explore Q53692 
Go to UniProtKB:  Q53692
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53692
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],
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],
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],
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

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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
  • Version 1.4: 2021-10-13
    Changes: Database references, Derived calculations