9DLT | pdb_00009dlt

STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE 5 FROM GLYCINE MAX CULTIVAR ESSEX COMPLEXED WITH PLP-GLYCINE

PDB DOI: https://doi.org/10.2210/pdb9DLT/pdb

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

Deposited: 2024-09-11 Released: 2025-09-17
Deposition Author(s): Beamer, L.J., Owuocha, L.F.
Funding Organization(s): National Science Foundation (NSF, United States), National Institute of Food and Agriculture (NIFA, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.231 (Depositor), 0.231 (DCC)
R-Value Work:
0.199 (Depositor), 0.201 (DCC)
R-Value Observed:
0.201 (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

Functional divergence of two soybean cytosolic serine hydroxymethyltransferases in development and defense against soybean cyst nematode.

Gamage, V.A., Owuocha, L.F., Lin, F., Li, Z., Beamer, L.J., Mitchum, M.G.

(2026) Front Plant Sci 17: 1942553-1942553

PubMed: 42729520 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fpls.2026.1942553
Primary Citation Related Structures:
9DLT

PubMed Abstract:
Serine hydroxymethyltransferase (SHMT) is an enzyme essential for one-carbon metabolism. In higher plants, multiple SHMT genes code for isoforms that function in the cytosol, nucleus, mitochondria, and chloroplasts. The soybean genome contains two cytosolic SHMT s, GmSHMT05 and GmSHMT08 , sharing high sequence identity and similar expression throughout soybean development. In certain soybean genotypes, two amino acid substitutions negatively impact GmSHMT08's ability to bind to tetrahydrofolate (THF), leading to a gain-of-function in resistance to the soybean cyst nematode (SCN). Whether this perturbation to the enzyme has other functional consequences for soybean growth and development remains unknown. Here, we investigated the roles of cytosolic GmSHMTs in soybean growth and development. We determined that the 3D structure and folate-binding affinity of GmSHMT05 are highly similar to the version of GmSHMT08 found in susceptible soybeans. We further measured phenotypic traits of two ethyl methanesulfonate-derived Gmshmt08 mutant plants in an SCN-resistant soybean background. Aboveground soybean growth and development were similar, except the Gmshmt08 mutant plants showed a significant increase in pods/plant in field phenotyping trials. Belowground analyses revealed a significant increase in lateral root and total root length in mutant plants, and CRISPR-Cas9 editing demonstrated an essential role of cytosolic SHMTs in root growth. Taken together, our results indicate that GmSHMT05 sustains overall soybean growth and development in the absence of GmSHMT08 ; however, GmSHMT08's gain-of-function in SCN resistance negatively influences pod and root growth, highlighting a potential trade-off between soybean defense and development that may impact yield when breeding with GmSHMT08 to develop SCN-resistant varieties.

Organizational Affiliation

Department of Plant Pathology and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States.

Macromolecule Content

Total Structure Weight: 329.89 kDa
Atom Count: 22,924
Modeled Residue Count: 2,786
Deposited Residue Count: 2,976
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, E A, B, C, D, E, F	496	Glycine max	Mutation(s): 0 Gene Names: 100815417, GLYMA_05G152100 EC: 2.1.2.1
UniProt
Find proteins for A0A0R4J3C9 (Glycine max) Explore A0A0R4J3C9 Go to UniProtKB: A0A0R4J3C9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0R4J3C9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLG (Subject of Investigation/LOI) Query on PLG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain O [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain O [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain O [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain G [auth A]	G [auth A] I [auth B] J [auth C] L [auth D] M [auth E] G [auth A], I [auth B], J [auth C], L [auth D], M [auth E], O [auth F]	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] C₁₀ H₁₅ N₂ O₇ P FEVQWBMNLWUBTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain O [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain O [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain K [auth C] SDF format, chain H [auth B] MOL2 format, chain N [auth E] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] mmCIF format, chain N [auth E] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B]	H [auth B], K [auth C], N [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth E] Interactions & Density Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.231 (Depositor), 0.231 (DCC)
R-Value Work: 0.199 (Depositor), 0.201 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.83	α = 90
b = 174.83	β = 90
c = 184.113	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	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: 2025-09-17

Deposition Author(s):

Beamer, L.J.

Owuocha, L.F.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2152548
National Institute of Food and Agriculture (NIFA, United States)	United States	021-67013-35887