8DL3

Crystal structure of the human queuine salvage enzyme DUF2419, complexed with queuine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate.

Hung, S.H.Elliott, G.I.Ramkumar, T.R.Burtnyak, L.McGrenaghan, C.J.Alkuzweny, S.Quaiyum, S.Iwata-Reuyl, D.Pan, X.Green, B.D.Kelly, V.P.de Crecy-Lagard, V.Swairjo, M.A.

(2023) Nucleic Acids Res 51: 935-951

  • DOI: https://doi.org/10.1093/nar/gkac1231
  • Primary Citation of Related Structures:  
    7U07, 7U1O, 7U5A, 7U91, 7UGK, 7UK3, 7ULC, 8DL3

  • PubMed Abstract: 

    Eukaryotic life benefits from-and ofttimes critically relies upon-the de novo biosynthesis and supply of vitamins and micronutrients from bacteria. The micronutrient queuosine (Q), derived from diet and/or the gut microbiome, is used as a source of the nucleobase queuine, which once incorporated into the anticodon of tRNA contributes to translational efficiency and accuracy. Here, we report high-resolution, substrate-bound crystal structures of the Sphaerobacter thermophilus queuine salvage protein Qng1 (formerly DUF2419) and of its human ortholog QNG1 (C9orf64), which together with biochemical and genetic evidence demonstrate its function as the hydrolase releasing queuine from queuosine-5'-monophosphate as the biological substrate. We also show that QNG1 is highly expressed in the liver, with implications for Q salvage and recycling. The essential role of this family of hydrolases in supplying queuine in eukaryotes places it at the nexus of numerous (patho)physiological processes associated with queuine deficiency, including altered metabolism, proliferation, differentiation and cancer progression.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Queuosine salvage protein
A, B
344Homo sapiensMutation(s): 0 
Gene Names: C9orf64
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T6V5 (Homo sapiens)
Explore Q5T6V5 
Go to UniProtKB:  Q5T6V5
PHAROS:  Q5T6V5
GTEx:  ENSG00000165118 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5T6V5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QEI (Subject of Investigation/LOI)
Query on QEI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
C12 H15 N5 O3
WYROLENTHWJFLR-ACLDMZEESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.726α = 90
b = 136.759β = 90.33
c = 52.606γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM70641
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110588-06A1

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2023-02-08
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description