8S3B | pdb_00008s3b

Crystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 3-(1H-Tetrazol-5-yl)benzoic acid and NAD

PDB DOI: https://doi.org/10.2210/pdb8S3B/pdb

Classification: OXIDOREDUCTASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-02-19 Released: 2024-09-04
Deposition Author(s): Grzechowiak, M., Ruszkowski, M.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.188 (Depositor), 0.191 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies.

Grzechowiak, M., Sliwiak, J., Link, A., Ruszkowski, M.

(2024) Int J Biol Macromol 278: 134648-134648

PubMed: 39142482 Search on PubMed
DOI: https://doi.org/10.1016/j.ijbiomac.2024.134648
Primary Citation Related Structures:
8S38, 8S39, 8S3A, 8S3B, 8S3C, 8S3D

PubMed Abstract:
Glutamate dehydrogenases (GDHs) are key enzymes at the crossroads of N and C metabolism in plants. Legumes, whose N metabolism is particularly intricate, possess a unique type of GDH. This study presents an analysis of a legume-type GDH (isoform 2) from Medicago truncatula (MtGDH2). We measured MtGDH2 activity in both the Glu → 2-oxoglutarate (2OG) and 2OG → Glu reaction directions and obtained kinetic parameters for Glu, 2OG, NAD ⁺, and NADH. Inhibition assays revealed that compounds possessing di- or tricarboxylates act as inhibitors of plant GDHs. Interestingly, 2,6-pyridinedicarboxylate (PYR) weakly inhibits MtGDH2 compared to Arabidopsis thaliana homologs. Furthermore, we explored tetrazole derivatives to discover 3-(1H-tetrazol-5-yl)benzoic acid (TBA) as an MtGDH2 inhibitor. The kinetic experiments are supported by six crystal structures, solved as: (i) unliganded enzyme, (ii) trapping the reaction intermediate 2-amino-2-hydroxyglutarate and NAD ⁺, and also complexed with NAD ⁺ and inhibitors such as (iii) citrate, (iv) PYR, (v) isophthalate, and (vi) TBA. The complex with TBA revealed a new mode of action that, in contrast to other inhibitors, prevents domain closure. This discovery points to TBA as a starting point for the development of novel GDH inhibitors to study the functions of GDH in plants and potentially boost biomass production.

Organizational Affiliation

Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.

Macromolecule Content

Total Structure Weight: 552.23 kDa
Atom Count: 39,595
Modeled Residue Count: 4,916
Deposited Residue Count: 4,968
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	414	Arabidopsis thaliana	Mutation(s): 0 Gene Names: 11433210, MTR_5g013470, MtrunA17_Chr5g0399821
UniProt
Find proteins for G7JYL4 (Medicago truncatula) Explore G7JYL4 Go to UniProtKB: G7JYL4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G7JYL4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain GC [auth K] SDF format, chain HB [auth G] SDF format, chain KA [auth C] SDF format, chain LC [auth L] SDF format, chain OB [auth H] SDF format, chain QA [auth D] SDF format, chain T [auth A] SDF format, chain UA [auth E] SDF format, chain WB [auth I] SDF format, chain YA [auth F] SDF format, chain DA [auth B] SDF format, chain AC [auth J] MOL2 format, chain GC [auth K] MOL2 format, chain HB [auth G] MOL2 format, chain KA [auth C] MOL2 format, chain LC [auth L] MOL2 format, chain OB [auth H] MOL2 format, chain QA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth E] MOL2 format, chain WB [auth I] MOL2 format, chain YA [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain AC [auth J] mmCIF format, chain GC [auth K] mmCIF format, chain HB [auth G] mmCIF format, chain KA [auth C] mmCIF format, chain LC [auth L] mmCIF format, chain OB [auth H] mmCIF format, chain QA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth E] mmCIF format, chain WB [auth I] mmCIF format, chain YA [auth F] mmCIF format, chain DA [auth B] mmCIF format, chain AC [auth J]	AC [auth J] DA [auth B] GC [auth K] HB [auth G] KA [auth C] AC [auth J], DA [auth B], GC [auth K], HB [auth G], KA [auth C], LC [auth L], OB [auth H], QA [auth D], T [auth A], UA [auth E], WB [auth I], YA [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AC [auth J] Focus chain DA [auth B] Focus chain GC [auth K] Focus chain HB [auth G] Focus chain KA [auth C] Focus chain LC [auth L] Focus chain OB [auth H] Focus chain QA [auth D] Focus chain T [auth A] Focus chain UA [auth E] Focus chain WB [auth I] Focus chain YA [auth F] Interactions & Density Focus chain AC [auth J] Focus chain DA [auth B] Focus chain GC [auth K] Focus chain HB [auth G] Focus chain KA [auth C] Focus chain LC [auth L] Focus chain OB [auth H] Focus chain QA [auth D] Focus chain T [auth A] Focus chain UA [auth E] Focus chain WB [auth I] Focus chain YA [auth F]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]
A1H40 (Subject of Investigation/LOI) Query on A1H40 Download:Ideal Coordinates CCD File SDF format, chain CC [auth K] SDF format, chain M [auth A] SDF format, chain NA [auth D] SDF format, chain W [auth B] SDF format, chain KB [auth H] SDF format, chain FA [auth C] MOL2 format, chain CC [auth K] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain KB [auth H] MOL2 format, chain FA [auth C] mmCIF format, chain CC [auth K] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain KB [auth H] mmCIF format, chain FA [auth C]	CC [auth K] FA [auth C] KB [auth H] M [auth A] NA [auth D] CC [auth K], FA [auth C], KB [auth H], M [auth A], NA [auth D], W [auth B]	3-(1~{H}-1,2,3,4-tetrazol-5-yl)benzoic acid C₈ H₆ N₄ O₂ MIERACSHCALJOM-UHFFFAOYSA-N		Interactions Focus chain CC [auth K] Focus chain FA [auth C] Focus chain KB [auth H] Focus chain M [auth A] Focus chain NA [auth D] Focus chain W [auth B] Interactions & Density Focus chain CC [auth K] Focus chain FA [auth C] Focus chain KB [auth H] Focus chain M [auth A] Focus chain NA [auth D] Focus chain W [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain Z [auth B]	Z [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain FC [auth K] SDF format, chain JC [auth L] SDF format, chain MA [auth D] SDF format, chain MB [auth H] SDF format, chain U [auth A] SDF format, chain RB [auth I] MOL2 format, chain CB [auth G] MOL2 format, chain FC [auth K] MOL2 format, chain JC [auth L] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth H] MOL2 format, chain U [auth A] MOL2 format, chain RB [auth I] mmCIF format, chain CB [auth G] mmCIF format, chain FC [auth K] mmCIF format, chain JC [auth L] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth H] mmCIF format, chain U [auth A] mmCIF format, chain RB [auth I]	CB [auth G] FC [auth K] JC [auth L] MA [auth D] MB [auth H] CB [auth G], FC [auth K], JC [auth L], MA [auth D], MB [auth H], RB [auth I], U [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain CB [auth G] Focus chain FC [auth K] Focus chain JC [auth L] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain RB [auth I] Focus chain U [auth A] Interactions & Density Focus chain CB [auth G] Focus chain FC [auth K] Focus chain JC [auth L] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain RB [auth I] Focus chain U [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain FB [auth G] SDF format, chain IA [auth C] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain WA [auth F] SDF format, chain SA [auth E] SDF format, chain NB [auth H] SDF format, chain GA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain IA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain WA [auth F] MOL2 format, chain SA [auth E] MOL2 format, chain NB [auth H] MOL2 format, chain GA [auth C] mmCIF format, chain FB [auth G] mmCIF format, chain IA [auth C] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain WA [auth F] mmCIF format, chain SA [auth E] mmCIF format, chain NB [auth H] mmCIF format, chain GA [auth C]	FB [auth G] GA [auth C] IA [auth C] NB [auth H] PA [auth D] FB [auth G], GA [auth C], IA [auth C], NB [auth H], PA [auth D], Q [auth A], SA [auth E], WA [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FB [auth G] Focus chain GA [auth C] Focus chain IA [auth C] Focus chain NB [auth H] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain SA [auth E] Focus chain WA [auth F] Interactions & Density Focus chain FB [auth G] Focus chain GA [auth C] Focus chain IA [auth C] Focus chain NB [auth H] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain SA [auth E] Focus chain WA [auth F]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth B] SDF format, chain DB [auth G] SDF format, chain DC [auth K] SDF format, chain EB [auth G] SDF format, chain JA [auth C] SDF format, chain KC [auth L] SDF format, chain LB [auth H] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QB [auth I] SDF format, chain R [auth A] SDF format, chain SB [auth I] SDF format, chain TA [auth E] SDF format, chain VB [auth I] SDF format, chain X [auth B] SDF format, chain XA [auth F] SDF format, chain Y [auth B] SDF format, chain ZA [auth F] SDF format, chain ZB [auth J] SDF format, chain UB [auth I] SDF format, chain TB [auth I] SDF format, chain S [auth A] SDF format, chain OA [auth D] SDF format, chain HC [auth K] SDF format, chain HA [auth C] SDF format, chain GB [auth G] SDF format, chain EC [auth K] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DB [auth G] MOL2 format, chain DC [auth K] MOL2 format, chain EB [auth G] MOL2 format, chain JA [auth C] MOL2 format, chain KC [auth L] MOL2 format, chain LB [auth H] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QB [auth I] MOL2 format, chain R [auth A] MOL2 format, chain SB [auth I] MOL2 format, chain TA [auth E] MOL2 format, chain VB [auth I] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth F] MOL2 format, chain ZB [auth J] MOL2 format, chain UB [auth I] MOL2 format, chain TB [auth I] MOL2 format, chain S [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain HC [auth K] MOL2 format, chain HA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain EC [auth K] mmCIF format, chain AA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DB [auth G] mmCIF format, chain DC [auth K] mmCIF format, chain EB [auth G] mmCIF format, chain JA [auth C] mmCIF format, chain KC [auth L] mmCIF format, chain LB [auth H] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QB [auth I] mmCIF format, chain R [auth A] mmCIF format, chain SB [auth I] mmCIF format, chain TA [auth E] mmCIF format, chain VB [auth I] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth B] mmCIF format, chain ZA [auth F] mmCIF format, chain ZB [auth J] mmCIF format, chain UB [auth I] mmCIF format, chain TB [auth I] mmCIF format, chain S [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain HC [auth K] mmCIF format, chain HA [auth C] mmCIF format, chain GB [auth G] mmCIF format, chain EC [auth K]	AA [auth B] CA [auth B] DB [auth G] DC [auth K] EB [auth G] AA [auth B], CA [auth B], DB [auth G], DC [auth K], EB [auth G], EC [auth K], GB [auth G], HA [auth C], HC [auth K], JA [auth C], KC [auth L], LB [auth H], N [auth A], O [auth A], OA [auth D], P [auth A], QB [auth I], R [auth A], S [auth A], SB [auth I], TA [auth E], TB [auth I], UB [auth I], VB [auth I], X [auth B], XA [auth F], Y [auth B], ZA [auth F], ZB [auth J]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CA [auth B] Focus chain DB [auth G] Focus chain DC [auth K] Focus chain EB [auth G] Focus chain EC [auth K] Focus chain GB [auth G] Focus chain HA [auth C] Focus chain HC [auth K] Focus chain JA [auth C] Focus chain KC [auth L] Focus chain LB [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain QB [auth I] Focus chain R [auth A] Focus chain S [auth A] Focus chain SB [auth I] Focus chain TA [auth E] Focus chain TB [auth I] Focus chain UB [auth I] Focus chain VB [auth I] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain ZA [auth F] Focus chain ZB [auth J] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth B] Focus chain DB [auth G] Focus chain DC [auth K] Focus chain EB [auth G] Focus chain EC [auth K] Focus chain GB [auth G] Focus chain HA [auth C] Focus chain HC [auth K] Focus chain JA [auth C] Focus chain KC [auth L] Focus chain LB [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain QB [auth I] Focus chain R [auth A] Focus chain S [auth A] Focus chain SB [auth I] Focus chain TA [auth E] Focus chain TB [auth I] Focus chain UB [auth I] Focus chain VB [auth I] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain ZA [auth F] Focus chain ZB [auth J]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain IC [auth K] SDF format, chain JB [auth G] SDF format, chain MC [auth L] SDF format, chain V [auth A] SDF format, chain VA [auth E] SDF format, chain YB [auth I] SDF format, chain RA [auth D] SDF format, chain PB [auth H] SDF format, chain LA [auth C] SDF format, chain EA [auth B] SDF format, chain BC [auth J] MOL2 format, chain BB [auth F] MOL2 format, chain IC [auth K] MOL2 format, chain JB [auth G] MOL2 format, chain MC [auth L] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth E] MOL2 format, chain YB [auth I] MOL2 format, chain RA [auth D] MOL2 format, chain PB [auth H] MOL2 format, chain LA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain BC [auth J] mmCIF format, chain BB [auth F] mmCIF format, chain IC [auth K] mmCIF format, chain JB [auth G] mmCIF format, chain MC [auth L] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth E] mmCIF format, chain YB [auth I] mmCIF format, chain RA [auth D] mmCIF format, chain PB [auth H] mmCIF format, chain LA [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain BC [auth J]	BB [auth F] BC [auth J] EA [auth B] IC [auth K] JB [auth G] BB [auth F], BC [auth J], EA [auth B], IC [auth K], JB [auth G], LA [auth C], MC [auth L], PB [auth H], RA [auth D], V [auth A], VA [auth E], YB [auth I]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain BC [auth J] Focus chain EA [auth B] Focus chain IC [auth K] Focus chain JB [auth G] Focus chain LA [auth C] Focus chain MC [auth L] Focus chain PB [auth H] Focus chain RA [auth D] Focus chain V [auth A] Focus chain VA [auth E] Focus chain YB [auth I] Interactions & Density Focus chain BB [auth F] Focus chain BC [auth J] Focus chain EA [auth B] Focus chain IC [auth K] Focus chain JB [auth G] Focus chain LA [auth C] Focus chain MC [auth L] Focus chain PB [auth H] Focus chain RA [auth D] Focus chain V [auth A] Focus chain VA [auth E] Focus chain YB [auth I]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain IB [auth G] SDF format, chain XB [auth I] SDF format, chain AB [auth F] MOL2 format, chain IB [auth G] MOL2 format, chain XB [auth I] MOL2 format, chain AB [auth F] mmCIF format, chain IB [auth G] mmCIF format, chain XB [auth I] mmCIF format, chain AB [auth F]	AB [auth F], IB [auth G], XB [auth I]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain IB [auth G] Focus chain XB [auth I] Interactions & Density Focus chain AB [auth F] Focus chain IB [auth G] Focus chain XB [auth I]