8TQF | pdb_00008tqf

Crystal structure of Soybean SHMT8 in complex with PLP-glycine and diglutamylated 5-formyltetrahydrofolate

PDB DOI: https://doi.org/10.2210/pdb8TQF/pdb

Classification: TRANSFERASE
Organism(s): Glycine max
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-07 Released: 2024-08-21
Deposition Author(s): Owuocha, L.F., Beamer, L.J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.214 (Depositor), 0.216 (DCC)
R-Value Work:
0.184 (Depositor), 0.188 (DCC)
R-Value Observed:
0.186 (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 binding of polyglutamylated tetrahydrofolate by serine hydroxymethyltransferase 8 from soybean.

Owuocha, L.F., Mitchum, M.G., Beamer, L.J.

(2024) Front Plant Sci 15: 1451839-1451839

PubMed: 39224855 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fpls.2024.1451839
Primary Citation Related Structures:
8TQF

PubMed Abstract:
Tetrahydrofolate and its derivatives participate in one-carbon transfer reactions in all organisms. The cellular form of tetrahydrofolate (THF) is modified by multiple glutamate residues and polyglutamylation plays a key role in organellar and cellular folate homeostasis. In addition, polyglutamylation of THF is known to increase the binding affinity to enzymes in the folate cycle, many of which can utilize polyglutamylated THF as a substrate. Here, we use X-ray crystallography to provide a high-resolution view of interactions between the enzyme serine hydroxymethyltransferase (SHMT), which provides one carbon precursors for the folate cycle, and a polyglutamylated form of THF. Our 1.7 Å crystal structure of soybean SHMT8 in complex with diglutamylated 5-formyl-THF reveals, for the first time, a structural rearrangement of a loop at the entrance to the folate binding site accompanied by the formation of novel specific interactions between the enzyme and the diglutamyl tail of the ligand. Biochemical assays show that additional glutamate moieties on the folate ligand increase both enzyme stability and binding affinity. Together these studies provide new information on SHMT structure and function and inform the design of anti-folate agents.

Organizational Affiliation

Department of Biochemistry, University of Missouri, Columbia, MO, United States.

Macromolecule Content

Total Structure Weight: 221.01 kDa
Atom Count: 16,518
Modeled Residue Count: 1,888
Deposited Residue Count: 1,968
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B, C, D	492	Glycine max	Mutation(s): 0 Gene Names: 100305380 EC: 2.1.2.1
UniProt
Find proteins for A0A0R0IK90 (Glycine max) Explore A0A0R0IK90 Go to UniProtKB: A0A0R0IK90
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0R0IK90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S8R (Subject of Investigation/LOI) Query on S8R Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	H [auth A], M [auth B], T [auth C], Y [auth D]	N-[4-({[(6R)-2-amino-5-formyl-4-hydroxy-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-glutamic acid C₂₅ H₃₀ N₈ O₁₀ QZHOZGNCYBQAQZ-PMPSAXMXSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D]
PLG Query on PLG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain W [auth D]	E [auth A], L [auth B], P [auth C], W [auth D]	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] C₁₀ H₁₅ N₂ O₇ P FEVQWBMNLWUBTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain W [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth D]	F [auth A] G [auth A] I [auth A] J [auth A] K [auth A] F [auth A], G [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], X [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth D]