6G60 | pdb_00006g60

Choline sulfatase from Ensifer (Sinorhizobium) meliloti cocrystalized with choline

PDB DOI: https://doi.org/10.2210/pdb6G60/pdb

Classification: HYDROLASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-03-30 Released: 2019-04-10
Deposition Author(s): Martinez-Rodriguez, S., Camara-Artigas, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.199 (Depositor), 0.172 (DCC)
R-Value Work:
0.169 (Depositor), 0.172 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.2 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

PubMed: 35503214 Search on PubMed Search on PubMed Central
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: 233.78 kDa
Atom Count: 17,304
Modeled Residue Count: 2,024
Deposited Residue Count: 2,032
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline-sulfatase	A, B, C, D	508	Sinorhizobium meliloti 1021	Mutation(s): 2 Gene Names: betC, R00949, SMc00127 EC: 3.1.6.6
UniProt
Find proteins for O69787 (Rhizobium meliloti (strain 1021)) Explore O69787 Go to UniProtKB: O69787
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O69787
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHT Query on CHT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	E [auth A], I [auth B], O [auth C], R [auth D]	CHOLINE ION C₅ H₁₄ N O OEYIOHPDSNJKLS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain O [auth C] Focus chain R [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C]	G [auth A] H [auth A] K [auth B] L [auth B] M [auth B] G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], Q [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain F [auth A]	F [auth A], J [auth B], P [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DDZ Query on DDZ	A, B, C, D	L-PEPTIDE LINKING	C₃ H₇ N O₄		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.199 (Depositor), 0.172 (DCC)
R-Value Work: 0.169 (Depositor), 0.172 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.538	α = 90
b = 206.898	β = 110.17
c = 116.602	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Martinez-Rodriguez, S.

Camara-Artigas, A.

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 2.0: 2019-04-24
Changes: Data collection, Polymer sequence
Version 2.1: 2023-03-08
Changes: Database references, Derived calculations
Version 2.2: 2024-11-13
Changes: Data collection, Derived calculations, Structure summary