8S3B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

Starting Model: experimental
View more details

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

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.134648
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
414Arabidopsis thalianaMutation(s): 0 
Gene Names: 11433210MTR_5g013470MtrunA17_Chr5g0399821
UniProt
Find proteins for G7JYL4 (Medicago truncatula)
Explore G7JYL4 
Go to UniProtKB:  G7JYL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7JYL4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
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
PG4
Query on PG4

Download Ideal Coordinates CCD File 
BA [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
A1H40 (Subject of Investigation/LOI)
Query on A1H40

Download Ideal Coordinates CCD File 
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
PGE
Query on PGE

Download Ideal Coordinates CCD File 
Z [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
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
PEG
Query on PEG

Download Ideal Coordinates CCD File 
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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
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
NA
Query on NA

Download Ideal Coordinates CCD File 
AB [auth F],
IB [auth G],
XB [auth I]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18150/KHDIXI
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.809α = 78.998
b = 109.861β = 78.482
c = 156.366γ = 72.219
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release