7NDW | pdb_00007ndw

ThyX-FADH2 soaked with 20 mM Formaldehyde

PDB DOI: https://doi.org/10.2210/pdb7NDW/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-02-02 Released: 2021-07-21
Deposition Author(s): Bou-Nader, C., Pecqueur, L., Hamdane, D.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.327 (Depositor), 0.233 (DCC)
R-Value Work:
0.270 (Depositor), 0.212 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

An enzymatic activation of formaldehyde for nucleotide methylation.

Bou-Nader, C., Stull, F.W., Pecqueur, L., Simon, P., Guerineau, V., Royant, A., Fontecave, M., Lombard, M., Palfey, B.A., Hamdane, D.

(2021) Nat Commun 12: 4542-4542

PubMed: 34315871 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-24756-8
Primary Citation Related Structures:
7NDW, 7NDZ

PubMed Abstract:
Folate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CH ₂O-shunt may be relevant in several other important folate-dependent reactions.

Organizational Affiliation

Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et Marie Curie, Paris, France.

Macromolecule Content

Total Structure Weight: 114.44 kDa
Atom Count: 7,404
Modeled Residue Count: 856
Deposited Residue Count: 928
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin-dependent thymidylate synthase	A, B, C, D	232	Thermotoga maritima	Mutation(s): 0 Gene Names: thyX, thy1, TM_0449 EC: 2.1.1.148
UniProt
Find proteins for Q9WYT0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYT0 Go to UniProtKB: Q9WYT0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WYT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HUF Query on HUF Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate C₂₈ H₃₅ N₉ O₁₆ P₂ KZQASMOVHMAAKH-MZWSMYJRSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
FDA (Subject of Investigation/LOI) Query on FDA Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	K [auth C], N [auth D]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain K [auth C] Focus chain N [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D]	F [auth A] I [auth B] J [auth B] P [auth D] Q [auth D] F [auth A], I [auth B], J [auth B], P [auth D], Q [auth D], R [auth D], S [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	H [auth B], L [auth C], O [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain H [auth B] Focus chain L [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.327 (Depositor), 0.233 (DCC)
R-Value Work: 0.270 (Depositor), 0.212 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.96	α = 90
b = 116.78	β = 90
c = 141.06	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Bou-Nader, C.

Pecqueur, L.

Hamdane, D.

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-11-IDEX-0004-02
Agence Nationale de la Recherche (ANR)	France	ANR-15-CE11-0004-01
Agence Nationale de la Recherche (ANR)	France	ANR-11-LABX-0011-01