Medicago truncatula HISN5 (IGPD) in complex with MN and IG2

Experimental Data Snapshot

  • Resolution: 2.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.0 of the entry. See complete history


Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting.

Witek, W.Sliwiak, J.Rawski, M.Ruszkowski, M.

(2024) Front Plant Sci 15: 1343980-1343980

  • DOI: https://doi.org/10.3389/fpls.2024.1343980
  • Primary Citation of Related Structures:  
    8QAV, 8QAW, 8QAX, 8QAY

  • PubMed Abstract: 

    The histidine biosynthetic pathway (HBP) is targeted for herbicide design with preliminary success only regarding imidazole-glycerol phosphate dehydratase (IGPD, EC, or HISN5, as referred to in plants. HISN5 catalyzes the sixth step of the HBP, in which imidazole-glycerol phosphate (IGP) is dehydrated to imidazole-acetol phosphate. In this work, we present high-resolution cryoEM and crystal structures of Medicago truncatula HISN5 ( Mt HISN5) in complexes with an inactive IGP diastereoisomer and with various other ligands. Mt HISN5 can serve as a new model for plant HISN5 structural studies, as it enables resolving protein-ligand interactions at high (2.2 Å) resolution using cryoEM. We identified ligand-binding hotspots and characterized the features of plant HISN5 enzymes in the context of the HISN5-targeted inhibitor design. Virtual screening performed against millions of small molecules not only revealed candidate molecules but also identified linkers for fragments that were experimentally confirmed to bind. Based on experimental and computational approaches, this study provides guidelines for designing symmetric HISN5 inhibitors that can reach two neighboring active sites. Finally, we conducted analyses of sequence similarity networks revealing that plant HISN5 enzymes derive from cyanobacteria. We also adopted a new approach to measure Mt HISN5 enzymatic activity using isothermal titration calorimetry and enzymatically synthesized IGP.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Imidazoleglycerol-phosphate dehydratase206Medicago truncatulaMutation(s): 0 
Find proteins for I3SDM5 (Medicago truncatula)
Explore I3SDM5 
Go to UniProtKB:  I3SDM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3SDM5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IG2 (Subject of Investigation/LOI)
Query on IG2

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CB [auth H]
DB [auth I]
EA [auth B]
AA [auth A],
BA [auth A],
CB [auth H],
DB [auth I],
EA [auth B],
FA [auth B],
FC [auth S],
GB [auth J],
HB [auth J],
IA [auth C],
JA [auth C],
MA [auth D],
MB [auth K],
NA [auth D],
NB [auth L],
QA [auth E],
QB [auth M],
RA [auth E],
SA [auth F],
TB [auth N],
VA [auth F],
YA [auth G],
YB [auth P],
ZA [auth G]
(2S,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate
C6 H11 N2 O6 P
Query on MN

Download Ideal Coordinates CCD File 
AB [auth H]
AC [auth P]
BB [auth H]
BC [auth Q]
CA [auth B]
AB [auth H],
AC [auth P],
BB [auth H],
BC [auth Q],
CA [auth B],
CC [auth Q],
DA [auth B],
DC [auth R],
EB [auth I],
EC [auth R],
FB [auth I],
GA [auth C],
GC [auth S],
HA [auth C],
HC [auth S],
IB [auth J],
IC [auth T],
JB [auth J],
JC [auth T],
KA [auth D],
KB [auth K],
KC [auth V],
LA [auth D],
LB [auth K],
LC [auth V],
MC [auth W],
NC [auth W],
OA [auth E],
OB [auth L],
OC [auth X],
PA [auth E],
PB [auth L],
PC [auth X],
QC [auth Y],
RB [auth M],
RC [auth Y],
SB [auth M],
TA [auth F],
UA [auth F],
UB [auth N],
VB [auth N],
WA [auth G],
WB [auth O],
XA [auth G],
XB [auth O],
Y [auth A],
Z [auth A],
ZB [auth P]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Polish National Science CentrePolandSonata 2018/31/D/NZ1/03630

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release