7U5A

Crystal structure of queuine salvage enzyme DUF2419 mutant K199C, complexed with queuosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 

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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
Queuine salvage enzyme DUF2419
A, B
331Sphaerobacter thermophilus DSM 20745Mutation(s): 1 
Gene Names: Sthe_2331
UniProt
Find proteins for D1C7A6 (Sphaerobacter thermophilus (strain DSM 20745 / S 6022))
Explore D1C7A6 
Go to UniProtKB:  D1C7A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1C7A6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QEO (Subject of Investigation/LOI)
Query on QEO

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-beta-D-ribofuranosyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
C17 H23 N5 O7
QQXQGKSPIMGUIZ-AEZJAUAXSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
D [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.401α = 90
b = 106.401β = 90
c = 159.643γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

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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