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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.160
R-Value Work: 0.148
R-Value Observed: 0.149

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Laboratory of Structural Biology, Department of Systems Life Sciences, Japan.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3UZZ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A3P Query on A3P Download Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	ADENOSINE-3'-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ WHTCPDAXWFLDIH-KQYNXXCUSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.160
R-Value Work: 0.148
R-Value Observed: 0.149
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-11-18

Deposition Author(s):

Revision History (Full details and data files)

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