2ZYW

crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAP and p-nitrophenol, obtained by two-step soaking method

• PDB DOI: https://doi.org/10.2210/pdb2ZYW/pdb

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


• Deposited: 2009-01-29 Released: 2009-04-21 
• Deposition Author(s): Teramoto, T., Sakakibara, Y., Liu, M.-C., Suiko, M., Kimura, M., Kakuta, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Snapshot of a Michaelis complex in a sulfuryl transfer reaction: Crystal structure of a mouse sulfotransferase, mSULT1D1, complexed with donor substrate and accepter substrate

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

(2009) Biochem Biophys Res Commun 383: 83-87

• PubMed: 19344693 
• DOI: https://doi.org/10.1016/j.bbrc.2009.03.146
• Primary Citation of Related Structures:  
  2ZYT, 2ZYU, 2ZYV, 2ZYW


• PubMed Abstract: 
  

  We report the crystal structure of mouse sulfotransferase, mSULT1D1, complexed with donor substrate 3'-phosphoadenosine 5'-phosphosulfate and accepter substrate p-nitrophenol. The structure is the first report of the native Michaelis complex of sulfotransferase. In the structure, three proposed catalytic residues (Lys48, Lys106, and His108) were in proper positions for engaging in the sulfuryl transfer reaction. The data strongly support that the sulfuryl transfer reaction proceeds through an S(N)2-like in-line displacement mechanism.

---

Organizational Affiliation: 

Department of Systems Life Sciences, Kyushu University, Hakozaki, Higashi-ku, 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: 36.11 kDa 
• Atom Count: 2,743 
• Modelled Residue Count: 289 
• 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
NPO	C [auth X], D [auth X]	P-NITROPHENOL C6 H5 N O3 BTJIUGUIPKRLHP-UHFFFAOYSA-N
GOL	E [auth X], F [auth X], G [auth X]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.313	α = 90
b = 67.838	β = 105.25
c = 42.867	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: 2009-04-21 
Deposition Author(s): Teramoto, T., Sakakibara, Y., Liu, M.-C., Suiko, M., Kimura, M., Kakuta, Y.

Revision History  

• Version 1.0: 2009-04-21
  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