3C7T

Crystal structure of the ecdysone phosphate phosphatase, EPPase, from Bombix mori in complex with tungstate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural and functional characterization of the c-terminal domain of the ecdysteroid phosphate phosphatase from Bombyx mori reveals a new enzymatic activity.

Chen, Y., Jakoncic, J., Wang, J., Zheng, X., Carpino, N., Nassar, N.

(2008) Biochemistry 47: 12135-12145

  • DOI: https://doi.org/10.1021/bi801318w
  • Primary Citation of Related Structures:  
    3C7T

  • PubMed Abstract: 

    • Here, we present the crystal structure of the ecdysone phosphate phosphatase (EPPase) phosphoglycerate mutase (PGM) homology domain, the first structure of a steroid phosphate phosphatase. The structure reveals an alpha/beta-fold common to members of the two histidine (2H)-phosphatase superfamily with strong homology to the Suppressor of T-cell receptor signaling-1 (Sts-1 PGM) protein ...

    Here, we present the crystal structure of the ecdysone phosphate phosphatase (EPPase) phosphoglycerate mutase (PGM) homology domain, the first structure of a steroid phosphate phosphatase. The structure reveals an alpha/beta-fold common to members of the two histidine (2H)-phosphatase superfamily with strong homology to the Suppressor of T-cell receptor signaling-1 (Sts-1 PGM) protein. The putative EPPase PGM active site contains signature residues shared by 2H-phosphatase enzymes, including a conserved histidine (His80) that acts as a nucleophile during catalysis. The physiological substrate ecdysone 22-phosphate was modeled in a hydrophobic cavity close to the phosphate-binding site. EPPase PGM shows limited substrate specificity with an ability to hydrolyze steroid phosphates, the phospho-tyrosine (pTyr) substrate analogue para-nitrophenylphosphate ( pNPP) and pTyr-containing peptides and proteins. Altogether, our data demonstrate a new protein tyrosine phosphatase (PTP) activity for EPPase. They suggest that EPPase and its closest homologues can be grouped into a distinct subfamily in the large 2H-phosphatase superfamily of proteins.

    Organizational Affiliation: 

    Department of Physiology and Biophysics, Stony Brook University, Basic Sciences Tower, Stony Brook, New York 11794-8661, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ecdysteroid-phosphate phosphataseA, B, C, D263Bombyx moriMutation(s): 0 
Gene Names: EPP
EC: 3.1.3 (UniProt), 3.1.3.48 (UniProt)
UniProt
Find proteins for Q7YTB0 (Bombyx mori)
Explore Q7YTB0 
Go to UniProtKB:  Q7YTB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7YTB0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WO4
Query on WO4
Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
Q [auth C],
V [auth D]		TUNGSTATE(VI)ION
O4 W
PBYZMCDFOULPGH-UHFFFAOYSA-N		 Ligand Interaction
IOD
Query on IOD
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K [auth B],
R [auth C],
S [auth C],
W [auth D],
X [auth D],
K [auth B],
R [auth C],
S [auth C],
W [auth D],
X [auth D],
Y [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
CL
Query on CL
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AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
O [auth B],
P [auth B],
T [auth C],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
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U [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
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N [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.901α = 90
b = 134.41β = 90
c = 135.188γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance