Crystal Structure of Medicago truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol

Experimental Data Snapshot

  • Resolution: 1.97 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD(+) Binding and the Cofactor Positioned to Accept a Hydride.

Ruszkowski, M.Dauter, Z.

(2017) Sci Rep 7: 10476-10476

  • DOI: https://doi.org/10.1038/s41598-017-10859-0
  • Primary Citation of Related Structures:  
    5VLB, 5VLC, 5VLD

  • PubMed Abstract: 

    Plants, lower eukaryotes, bacteria, and archaebacteria synthesise L-histidine (His) in a similar, multistep pathway that is absent in mammals. This makes the His biosynthetic route a promising target for herbicides, antifungal agents, and antibiotics. The last enzyme of the pathway, bifunctional L-histidinol dehydrogenase (HDH, EC, catalyses two oxidation reactions: from L-histidinol (HOL) to L-histidinaldehyde and from L-histidinaldehyde to His. Over the course of the reaction, HDH utilises two molecules of NAD + as the hydride acceptor. The object of this study was the HDH enzyme from the model legume plant, Medicago truncatula (MtHDH). Three crystal structures complexed with imidazole, HOL, and His with NAD + provided in-depth insights into the enzyme architecture, its active site, and the cofactor binding mode. The overall structure of MtHDH is similar to the two bacterial orthologues whose three-dimensional structures have been determined. The three snapshots, with the MtHDH enzyme captured in different states, visualise structural rearrangements that allow for NAD + binding for the first time. Furthermore, the MtHDH complex with His and NAD + displays the cofactor molecule situated in a way that would allow for a hydride transfer.

  • Organizational Affiliation

    Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA. milosz.ruszkowski@nih.gov.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidinol dehydrogenase, chloroplastic
A, B, C, D, E
A, B, C, D, E, F
446Medicago truncatulaMutation(s): 0 
Gene Names: MTR_2g030520
Find proteins for G7IKX3 (Medicago truncatula)
Explore G7IKX3 
Go to UniProtKB:  G7IKX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7IKX3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HSO

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
G [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
C6 H12 N3 O
Query on ZN

Download Ideal Coordinates CCD File 
H [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
H [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth E]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.97 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.859α = 90
b = 139.201β = 119.18
c = 102.692γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Structure summary
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection