2ZVQ

Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAP and alpha-naphthol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


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


Literature

Structural basis for the broad range substrate specificity of a novel mouse cytosolic sulfotransferase--mSULT1D1

Teramoto, T., Sakakibara, Y., Liu, M.-C., Suiko, M., Kimura, M., Kakuta, Y.

(2009) Biochem Biophys Res Commun 379: 76-80

  • DOI: 10.1016/j.bbrc.2008.12.013
  • Primary Citation of Related Structures:  
    2ZVP, 2ZVQ

  • PubMed Abstract: 

    • The mouse cytosolic sulfotransferase, mSULT1D1, catalyzes the sulfonation of a wide range of phenolic molecules including p-nitrophenol (pNP), alpha-naphthol (alphaNT), serotonin, as well as dopamine and its metabolites. To gain insight into the stru ...

    The mouse cytosolic sulfotransferase, mSULT1D1, catalyzes the sulfonation of a wide range of phenolic molecules including p-nitrophenol (pNP), alpha-naphthol (alphaNT), serotonin, as well as dopamine and its metabolites. To gain insight into the structural basis for its broad range substrate specificity, we solved two distinct ternary crystal structures of mSULT1D1, complexed with 3'-phosphoadenosine-5'-phosphate (PAP) plus pNP or PAP plus alphaNT. The structures revealed that the mSULT1D1 contains an L-shaped accepter-binding site which comprises 20 amino acid residues and four conserved water molecules. The shape of the accepter-binding site can be adjusted by conformational changes of two residues, Ile148 and Glu247, upon binding with respective substrates.

    Organizational Affiliation: 

    Department of Systems Life Sciences, Laboratory of Structural Biology, Graduate School, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-ester sulfotransferaseX295Mus musculusMutation(s): 0 
Gene Names: Sult1d1, St1d1
EC: 2.8.2.9 (PDB Primary Data), 2.8.2 (UniProt)
Find proteins for Q3UZZ6 (Mus musculus)
Explore Q3UZZ6 
Go to UniProtKB:  Q3UZZ6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A3P
Query on A3P
Download Ideal Coordinates CCD File 
X
ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N		 Ligand Interaction
1NP
Query on 1NP
Download Ideal Coordinates CCD File 
X
1-NAPHTHOL
C10 H8 O
KJCVRFUGPWSIIH-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
X
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.178α = 90
b = 67.49β = 105.47
c = 42.821γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
BBSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance