7PTJ | pdb_00007ptj

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

PDB DOI: https://doi.org/10.2210/pdb7PTJ/pdb

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

Deposited: 2021-09-27 Released: 2022-08-03
Deposition Author(s): Gavira, J.A., Martinez-Rodriguez, S.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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: 242.15 kDa
Atom Count: 18,789
Modeled Residue Count: 2,045
Deposited Residue Count: 2,080
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	520	Sinorhizobium meliloti	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O69787
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE (Subject of Investigation/LOI) Query on EPE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain NA [auth D] SDF format, chain Z [auth C] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain P [auth B]	E [auth A], F [auth A], NA [auth D], P [auth B], Z [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain NA [auth D] Focus chain P [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain NA [auth D] Focus chain P [auth B] Focus chain Z [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain Q [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], OA [auth D], PA [auth D], Q [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain Q [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	FA [auth C] GA [auth C] HA [auth C] IA [auth C] JA [auth C] FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain QA [auth D] SDF format, chain Y [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain Y [auth B]	MA [auth C], N [auth A], QA [auth D], Y [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain MA [auth C] Focus chain N [auth A] Focus chain QA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain MA [auth C] Focus chain N [auth A] Focus chain QA [auth D] Focus chain Y [auth B]