4G09 | pdb_00004g09

The crystal structure of the C366S mutant of HDH from Brucella suis in complex with a substituted benzyl ketone

• PDB DOI: https://doi.org/10.2210/pdb4G09/pdb

• Classification: Oxidoreductase/Oxidoreductase inhibitor
• Organism(s): Brucella suis 1330
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-07-09 Released: 2013-10-02 
• Deposition Author(s): D'Ambrosio, K., De Simone, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Structural basis for the rational design of new anti-Brucella agents: The crystal structure of the C366S mutant of l-histidinol dehydrogenase from Brucella suis.

D'ambrosio, K., Lopez, M., Dathan, N.A., Ouahrani-Bettache, S., Kohler, S., Ascione, G., Monti, S.M., Winum, J.Y., De Simone, G.

(2014) Biochimie 97: 114-120

• PubMed: 24140957 
• DOI: https://doi.org/10.1016/j.biochi.2013.09.028
• Primary Citation Related Structures: 
  4G07, 4G09


• PubMed Abstract: 
  

  L-Histidinol dehydrogenase from Brucella suis (BsHDH) is an enzyme involved in the histidine biosynthesis pathway which is absent in mammals, thus representing a very interesting target for the development of anti-Brucella agents. In this paper we report the crystallographic structure of a mutated form of BsHDH both in its unbound form and in complex with a nanomolar inhibitor. These studies provide the first structural background for the rational design of potent HDH inhibitors, thus offering new hints for clinical applications.

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Organizational Affiliation: 
• Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-UM1-UM2, Bâtiment de Recherche Max Mousseron, Ecole Nationale Supérieure de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex, France; Centre d'Etudes d'Agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236 CNRS-UM1-UM2, 1919 Route de Mende, 34293 Montpellier, France.
Centre d'Etudes d'Agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236 CNRS-UM1-UM2, 1919 Route de Mende, 34293 Montpellier, France.
Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Napoli, Italy. Electronic address: [e-mail].
Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-UM1-UM2, Bâtiment de Recherche Max Mousseron, Ecole Nationale Supérieure de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex, France.
Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Napoli, Italy. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.82 kDa 
• Atom Count: 3,544 
• Modeled Residue Count: 432 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidinol dehydrogenase	A	438	Brucella suis 1330	Mutation(s): 1  Gene Names: hisD, BR0252, BS1330_I0253 EC: 1.1.1.23
UniProt
Find proteins for Q8G2R2 (Brucella suis biovar 1 (strain 1330)) Explore Q8G2R2  Go to UniProtKB:  Q8G2R2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0VD	F [auth A]	(3S)-3-amino-1-[4-(benzyloxy)phenyl]-4-(1H-imidazol-4-yl)butan-2-one C20 H21 N3 O2 JPAWSYOZOLVNBT-IBGZPJMESA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.654	α = 90
b = 105.072	β = 90
c = 111.25	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): D'Ambrosio, K., De Simone, G.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-11-06
  Changes: Database references
• Version 1.2: 2014-02-05
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations