2ZVQ

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

• PDB DOI: https://doi.org/10.2210/pdb2ZVQ/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-11-14 Released: 2008-12-30 
• Deposition Author(s): Teramoto, T., Sakakibara, Y., Liu, M.-C., Suiko, M., Kimura, M., Kakuta, Y.

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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 

Starting Model: experimental

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

• PubMed: 19073143 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.03 kDa 
• Atom Count: 3,099 
• Modelled Residue Count: 288 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-ester sulfotransferase	A [auth X]	295	Mus musculus	Mutation(s): 0  Gene Names: Sult1d1 EC: 2.8.2.9 (PDB Primary Data), 2.8.2 (UniProt)
UniProt
Find proteins for Q3UZZ6 (Mus musculus) Explore Q3UZZ6  Go to UniProtKB:  Q3UZZ6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P	B [auth X]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N
1NP	C [auth X], D [auth X]	1-NAPHTHOL C10 H8 O KJCVRFUGPWSIIH-UHFFFAOYSA-N
GOL	E [auth X], F [auth X]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 156.178	α = 90
b = 67.49	β = 105.47
c = 42.821	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BBS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-30 
Deposition Author(s): Teramoto, T., Sakakibara, Y., Liu, M.-C., Suiko, M., Kimura, M., Kakuta, Y.

Revision History  

• Version 1.0: 2008-12-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description