7PTH | pdb_00007pth

C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound to choline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7PTH

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding.

Gavira, J.A.Camara-Artigas, A.Neira, J.L.Torres de Pinedo, J.M.Sanchez, P.Ortega, E.Martinez-Rodriguez, S.

(2022) Acta Crystallogr D Struct Biol 78: 669-682

  • DOI: https://doi.org/10.1107/S2059798322003709
  • Primary Citation Related Structures: 
    6G5Z, 6G60, 7PTH, 7PTJ

  • PubMed Abstract: 

    Choline-O-sulfatase (COSe; EC 3.1.6.6) is a member of the alkaline phosphatase (AP) superfamily, and its natural function is to hydrolyze choline-O-sulfate into choline and sulfate. Despite its natural function, the major interest in this enzyme resides in the landmark catalytic/substrate promiscuity of sulfatases, which has led to attention in the biotechnological field due to their potential in protein engineering. In this work, an in-depth structural analysis of wild-type Sinorhizobium (Ensifer) meliloti COSe (SmeCOSe) and its C54S active-site mutant is reported. The binding mode of this AP superfamily member to both products of the reaction (sulfate and choline) and to a substrate-like compound are shown for the first time. The structures further confirm the importance of the C-terminal extension of the enzyme in becoming part of the active site and participating in enzyme activity through dynamic intra-subunit and inter-subunit hydrogen bonds (Asn146 A -Asp500 B -Asn498 B ). These residues act as the `gatekeeper' responsible for the open/closed conformations of the enzyme, in addition to assisting in ligand binding through the rearrangement of Leu499 (with a movement of approximately 5 Å). Trp129 and His145 clamp the quaternary ammonium moiety of choline and also connect the catalytic cleft to the C-terminus of an adjacent protomer. The structural information reported here contrasts with the proposed role of conformational dynamics in promoting the enzymatic catalytic proficiency of an enzyme.


  • Organizational Affiliation
    • Laboratorio de Estudios Cristalográficos, CSIC, Armilla, 18100 Granada, Spain.

Macromolecule Content 

  • Total Structure Weight: 238.91 kDa 
  • Atom Count: 19,114 
  • Modeled Residue Count: 2,058 
  • Deposited Residue Count: 2,080 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Choline sulfatase
A, B, C, D
520Sinorhizobium melilotiMutation(s): 1 
EC: 3.1.6.6
UniProt
Find proteins for O69787 (Rhizobium meliloti (strain 1021))
Explore O69787 
Go to UniProtKB:  O69787
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO69787
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
M [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CHT
(Subject of Investigation/LOI)

Query on CHT



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
K [auth C],
O [auth D]
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
L [auth C],
P [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
H [auth B],
I [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
N [auth C],
Q [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.773α = 90
b = 103.973β = 104.037
c = 108.966γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
REFMACrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-116261GB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description