2ZYV | pdb_00002zyv

Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAPS/PAP and p-nitrophenol

PDB DOI: https://doi.org/10.2210/pdb2ZYV/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: 1.81 Å
R-Value Free:
0.203 (Depositor), 0.202 (DCC)
R-Value Work:
0.179 (Depositor), 0.178 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2009.03.146
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 36.47 kDa
Atom Count: 2,778
Modeled Residue Count: 289
Deposited Residue Count: 295
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3UZZ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PPS Query on PPS 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]	3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE C₁₀ H₁₅ N₅ O₁₃ P₂ S GACDQMDRPRGCTN-KQYNXXCUSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
NPO Query on NPO Download:Ideal Coordinates CCD File SDF format, chain D [auth X] SDF format, chain C [auth X] MOL2 format, chain D [auth X] MOL2 format, chain C [auth X] mmCIF format, chain D [auth X] mmCIF format, chain C [auth X]	C [auth X], D [auth X]	P-NITROPHENOL C₆ H₅ N O₃ BTJIUGUIPKRLHP-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Focus chain D [auth X] Interactions & Density Focus chain C [auth X] Focus chain D [auth X]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth X] SDF format, chain G [auth X] SDF format, chain H [auth X] SDF format, chain I [auth X] SDF format, chain J [auth X] SDF format, chain F [auth X] MOL2 format, chain E [auth X] MOL2 format, chain G [auth X] MOL2 format, chain H [auth X] MOL2 format, chain I [auth X] MOL2 format, chain J [auth X] MOL2 format, chain F [auth X] mmCIF format, chain E [auth X] mmCIF format, chain G [auth X] mmCIF format, chain H [auth X] mmCIF format, chain I [auth X] mmCIF format, chain J [auth X] mmCIF format, chain F [auth X]	E [auth X] F [auth X] G [auth X] H [auth X] I [auth X] E [auth X], F [auth X], G [auth X], H [auth X], I [auth X], J [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Interactions & Density Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.203 (Depositor), 0.202 (DCC)
R-Value Work: 0.179 (Depositor), 0.178 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.241	α = 90
b = 67.793	β = 105.23
c = 42.904	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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Entry History

Deposition Data

Released Date: 2009-04-21

Deposition Author(s):

Revision History (Full details and data files)

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