3WKY | pdb_00003wky

Crystal structure of hemolymph type prophenoloxidase (proPOb) from crustacean


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.196 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

The crystal structure of a crustacean prophenoloxidase provides a clue to understanding the functionality of the type 3 copper proteins.

Masuda, T.Momoji, K.Hirata, T.Mikami, B.

(2014) FEBS J 281: 2659-2673

  • DOI: https://doi.org/10.1111/febs.12812
  • Primary Citation Related Structures: 
    3WKY

  • PubMed Abstract: 

    Phenoloxidase (PO), which is classified as a type 3 copper protein, catalyzes the hydroxylation of monophenol to o-diphenol and subsequent oxidation to the corresponding o-quinone. The geometry and coordination environment of the active site of the arthropod PO are very similar to those of the arthropod hemocyanin (Hc). However, unlike the POs, Hc is an oxygen carrier in crustaceans, and does not possess PO activity in general. Recently, we identified a new type of proPO from a crustacean and designated it proPOβ. This enzyme has many characteristics that are rather similar to those of Hc, such as its maturation, localization, and oligomeric state. Here, we determined the crystal structure of proPOβ prepared from the hemolymph of kuruma prawns (Marsupenaeus japonicus) at 1.8-Å resolution. M. japonicus proPOβ forms a homohexamer rather similar to that of arthropod Hc. The geometry of the active copper site in proPOβ is nearly identical to that of arthropod Hc. Furthermore, the well-characterized 'place-holder' phenylalanine is present (Phe72). However, the accessibility to the active site differs in several ways. First, another phenylalanine, which shields the active site by interacting with a copper-coordinated histidine in crustacean Hc, is replaced by valine in the proPOβ structure. Second, two tyrosines, Tyr208 and Tyr209, both of which are absent in Hc, show the alternative conformations and form a pathway providing access to the reaction center. Thus, the present crystal structure clarifies the similarities and differences in the activity of two closely related proteins, PO and Hc. Structural data are available in the RSCB protein data bank under the accession number 3WKY. ray crystallography (View interaction).


  • Organizational Affiliation
    • Laboratory of Food Quality Design and Development, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Japan.

Macromolecule Content 

  • Total Structure Weight: 161.96 kDa 
  • Atom Count: 12,734 
  • Modeled Residue Count: 1,310 
  • Deposited Residue Count: 1,374 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prophenoloxidase b
A, B
687Penaeus japonicusMutation(s): 0 
UniProt
Find proteins for G5EKM4 (Penaeus japonicus)
Explore G5EKM4 
Go to UniProtKB:  G5EKM4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG5EKM4
Glycosylation
Glycosylation Sites: 6
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CUO

Query on CUO



Download:Ideal Coordinates CCD File
J [auth A],
Z [auth B]
CU2-O2 CLUSTER
Cu2 O2
PCGDDKBKPXANNY-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
K [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
FA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
EA [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
P [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.706α = 90
b = 156.706β = 90
c = 283.83γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2022-08-24
    Changes: Database references, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Data collection, Structure summary