Crystal Structure of Brugia malayi Deoxyhypusine synthase (DHPS)

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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Structural features and development of an assay platform of the parasite target deoxyhypusine synthase of Brugia malayi and Leishmania major.

Silva, S.F.Klippel, A.H.Ramos, P.Z.Santiago, A.D.S.Valentini, S.R.Bengtson, M.H.Massirer, K.B.Bilsland, E.Counago, R.M.Zanelli, C.F.

(2020) PLoS Negl Trop Dis 14: e0008762-e0008762

  • DOI: https://doi.org/10.1371/journal.pntd.0008762
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Deoxyhypusine synthase (DHS) catalyzes the first step of the post-translational modification of eukaryotic translation factor 5A (eIF5A), which is the only known protein containing the amino acid hypusine. Both proteins are essential for eukaryotic cell viability, and DHS has been suggested as a good candidate target for small molecule-based therapies against eukaryotic pathogens. In this work, we focused on the DHS enzymes from Brugia malayi and Leishmania major, the causative agents of lymphatic filariasis and cutaneous leishmaniasis, respectively. To enable B. malayi (Bm)DHS for future target-based drug discovery programs, we determined its crystal structure bound to cofactor NAD+. We also reported an in vitro biochemical assay for this enzyme that is amenable to a high-throughput screening format. The L. major genome encodes two DHS paralogs, and attempts to produce them recombinantly in bacterial cells were not successful. Nevertheless, we showed that ectopic expression of both LmDHS paralogs can rescue yeast cells lacking the endogenous DHS-encoding gene (dys1). Thus, functionally complemented dys1Δ yeast mutants can be used to screen for new inhibitors of the L. major enzyme. We used the known human DHS inhibitor GC7 to validate both in vitro and yeast-based DHS assays. Our results show that BmDHS is a homotetrameric enzyme that shares many features with its human homologue, whereas LmDHS paralogs are likely to form a heterotetrameric complex and have a distinct regulatory mechanism. We expect our work to facilitate the identification and development of new DHS inhibitors that can be used to validate these enzymes as vulnerable targets for therapeutic interventions against B. malayi and L. major infections.

  • Organizational Affiliation

    Chemistry Institute, São Paulo State University-UNESP, Araraquara, SP, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BMA-DHPS-1, isoform a
A, B, C, D
367Brugia malayiMutation(s): 0 
Gene Names: bma-dhps-1Bm1_16300Bma-dhps-1Bm14681BM_Bm14681
Find proteins for A0A0J9XTC4 (Brugia malayi)
Explore A0A0J9XTC4 
Go to UniProtKB:  A0A0J9XTC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9XTC4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C]
C21 H27 N7 O14 P2
Query on GOL

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F [auth A],
H [auth B],
K [auth C],
L [auth D],
M [auth D]
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.753α = 90
b = 136.32β = 92.92
c = 75.883γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil13/50724-5
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil465651/2014-3
Sao Paulo Research Foundation (FAPESP)Brazil2014/50897-0

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description