6EZA

Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases.

Bou-Nader, C.Bregeon, D.Pecqueur, L.Fontecave, M.Hamdane, D.

(2018) Biochemistry 57: 5407-5414

  • DOI: https://doi.org/10.1021/acs.biochem.8b00584
  • Primary Citation of Related Structures:  
    6EZA, 6EZB, 6EZC

  • PubMed Abstract: 

    Dihydrouridine (D) is an abundant modified base of tRNA found in the majority of living organisms. This base is synthesized via an NADPH-dependent reduction of specific uridines by the dihydrouridine synthases (Dus), a large family of flavoenzymes comprising eight subfamilies. Almost all of these enzymes function with only two conserved domains, an N-terminal catalytic domain (TBD) adopting a TIM barrel fold and a unique C-terminal helical domain (HD) devoted to tRNA recognition, except for the animal U20-specific Dus2 enzyme. Curiously, this enzyme is distinguished from paralogues and its fungi orthologues by the acquisition of an additional domain, a double stranded RNA binding domain (dsRBD), which serves as the main tRNA binding module. On the basis of a homology model of yeast Dus2 and the crystallographic structure of a human Dus2 variant (TBD + HD) lacking dsRBD, we herein show that the HD surface of the human enzyme is less electropositive than that of its yeast orthologue. This is partly due to two positively charged residues, K304 and K315, present in yeast and more broadly in fungi Dus2 that are replaced by E294 and Q305 in human and conserved among animals Dus2. By artificially reintroducing these positive charges in human Dus2 lacking dsRBD, we restored a functional tRNA binding in this enzyme variant. Altogether, these results suggest that the electrostatic potential changes of HD have likely played a key role in the emergence of a new tRNA binding mode among Dus2 enzymes.


  • Organizational Affiliation

    Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229 , Collège De France , 11 place Marcelin Berthelot , Paris 75231 Cedex 05 , France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
A, B
327Homo sapiensMutation(s): 1 
Gene Names: DUS2DUS2L
EC: 1.3.1 (PDB Primary Data), 1.3.1.91 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX74 (Homo sapiens)
Explore Q9NX74 
Go to UniProtKB:  Q9NX74
PHAROS:  Q9NX74
GTEx:  ENSG00000167264 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NX74
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth A]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth A],
K [auth B],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.47α = 90
b = 77.11β = 91.99
c = 84.48γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE11-0004-01
French National Research AgencyFranceANR-11-LABX-0011-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description