2ZPT

Crystal structure of mouse sulfotransferase SULT1D1 complex with PAP

• PDB DOI: https://doi.org/10.2210/pdb2ZPT/pdb

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


• Deposited: 2008-07-28 Released: 2008-11-18 
• Deposition Author(s): Teramoto, T., Sakakibara, Y., Inada, K., Liu, M.C., Suiko, M., Kimura, M., Kakuta, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mSULT1D1, a mouse catecholamine sulfotransferase

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

(2008) FEBS Lett 582: 3909-3914

• PubMed: 18977225 
• DOI: https://doi.org/10.1016/j.febslet.2008.10.035
• Primary Citation of Related Structures:  
  2ZPT


• PubMed Abstract: 
  

  In mammals, sulfonation as mediated by specific cytosolic sulfotransferases (SULTs) plays an important role in the homeostasis of dopamine and other catecholamines. To gain insight into the structural basis for dopamine recognition/binding, we determined the crystal structure of a mouse dopamine-sulfating SULT, mouse SULT1D1 (mSULT1D1). Data obtained indicated that mSULT1D1 comprises of a single alpha/beta domain with a five-stranded parallel beta-sheet. In contrast to the structure of the human SULT1A3 (hSULT1A3)-dopamine complex previously reported, molecular modeling and mutational analysis revealed that a water molecule plays a critical role in the recognition of the amine group of dopamine by mSULT1D1. These results imply differences in substrate binding between dopamine-sulfating SULTs from different species.

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Organizational Affiliation: 

Laboratory of Structural Biology, Department of Systems Life Sciences, 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: 35.65 kDa 
• Atom Count: 3,162 
• 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 2 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
GOL	C [auth X]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.819	α = 90
b = 67.6	β = 105.63
c = 42.696	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: 2008-11-18 
Deposition Author(s): Teramoto, T., Sakakibara, Y., Inada, K., Liu, M.C., Suiko, M., Kimura, M., Kakuta, Y.

Revision History  

• Version 1.0: 2008-11-18
  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