3UWL | pdb_00003uwl

Crystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with 5-formyl tetrahydrofolate

PDB DOI: https://doi.org/10.2210/pdb3UWL/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-12-02 Released: 2012-08-29
Deposition Author(s): Pozzi, C., Catalano, A., Cortesi, D., Luciani, R., Ferrari, S., Fritz, T., Costi, M.P., Mangani, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.217 (Depositor), 0.217 (DCC)
R-Value Work:
0.160 (Depositor), 0.162 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

The structure of Enterococcus faecalis thymidylate synthase provides clues about folate bacterial metabolism.

Pozzi, C., Ferrari, S., Cortesi, D., Luciani, R., Stroud, R.M., Catalano, A., Costi, M.P., Mangani, S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1232-1241

PubMed: 22948925 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S0907444912026236
Primary Citation Related Structures:
3UWL

PubMed Abstract:
Drug resistance to therapeutic antibiotics poses a challenge to the identification of novel targets and drugs for the treatment of infectious diseases. Infections caused by Enterococcus faecalis are a major health problem. Thymidylate synthase (TS) from E. faecalis is a potential target for antibacterial therapy. The X-ray crystallographic structure of E. faecalis thymidylate synthase (EfTS), which was obtained as a native binary complex composed of EfTS and 5-formyltetrahydrofolate (5-FTHF), has been determined. The structure provides evidence that EfTS is a half-of-the-sites reactive enzyme, as 5-FTHF is bound to two of the four independent subunits present in the crystal asymmetric unit. 5-FTHF is a metabolite of the one-carbon transfer reaction catalysed by 5-formyltetrahydrofolate cyclo-ligase. Kinetic studies show that 5-FTHF is a weak inhibitor of EfTS, suggesting that the EfTS-5-FTHF complex may function as a source of folates and/or may regulate one-carbon metabolism. The structure represents the first example of endogenous 5-FTHF bound to a protein involved in folate metabolism.

Organizational Affiliation

Dipartimento di Chimica, University of Siena, Siena, Italy.

Macromolecule Content

Total Structure Weight: 147.72 kDa
Atom Count: 10,751
Modeled Residue Count: 1,204
Deposited Residue Count: 1,260
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, C	315	Enterococcus faecalis	Mutation(s): 0 Gene Names: EF_1576, thyA EC: 2.1.1.45
UniProt
Find proteins for Q834R3 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q834R3 Go to UniProtKB: Q834R3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q834R3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	B, D	315	Enterococcus faecalis	Mutation(s): 0 Gene Names: EF_1576, thyA EC: 2.1.1.45
UniProt
Find proteins for Q834R3 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q834R3 Go to UniProtKB: Q834R3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q834R3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FFO Query on FFO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain Q [auth D] MOL2 format, chain G [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain G [auth B] mmCIF format, chain Q [auth D]	G [auth B], Q [auth D]	N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid C₂₀ H₂₃ N₇ O₇ VVIAGPKUTFNRDU-STQMWFEESA-N		Interactions Focus chain G [auth B] Focus chain Q [auth D] Interactions & Density Focus chain G [auth B] Focus chain Q [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain P [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain P [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain P [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain E [auth B]	E [auth B] F [auth B] H [auth B] O [auth C] P [auth D] E [auth B], F [auth B], H [auth B], O [auth C], P [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain H [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain H [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain R [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain N [auth C]	I [auth B] J [auth B] K [auth B] L [auth B] M [auth C] I [auth B], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain S [auth D] Focus chain T [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	B, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.217 (Depositor), 0.217 (DCC)
R-Value Work: 0.160 (Depositor), 0.162 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.94	α = 90
b = 94.25	β = 95.01
c = 96.19	γ = 90

Software Package:

Software Name	Purpose
PXSOFT	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2013-01-23
Changes: Database references
Version 2.0: 2019-11-20
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.2: 2024-10-30
Changes: Structure summary