6ZK7

Crystal Structure of human PYROXD1/FAD complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The oxidoreductase PYROXD1 uses NAD(P) + as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response.

Asanovic, I.Strandback, E.Kroupova, A.Pasajlic, D.Meinhart, A.Tsung-Pin, P.Djokovic, N.Anrather, D.Schuetz, T.Suskiewicz, M.J.Sillamaa, S.Kocher, T.Beveridge, R.Nikolic, K.Schleiffer, A.Jinek, M.Hartl, M.Clausen, T.Penninger, J.Macheroux, P.Weitzer, S.Martinez, J.

(2021) Mol Cell 81: 2520

  • DOI: https://doi.org/10.1016/j.molcel.2021.04.007
  • Primary Citation of Related Structures:  
    6ZK7

  • PubMed Abstract: 

    The tRNA ligase complex (tRNA-LC) splices precursor tRNAs (pre-tRNA), and Xbp1-mRNA during the unfolded protein response (UPR). In aerobic conditions, a cysteine residue bound to two metal ions in its ancient, catalytic subunit RTCB could make the tRNA-LC susceptible to oxidative inactivation. Here, we confirm this hypothesis and reveal a co-evolutionary association between the tRNA-LC and PYROXD1, a conserved and essential oxidoreductase. We reveal that PYROXD1 preserves the activity of the mammalian tRNA-LC in pre-tRNA splicing and UPR. PYROXD1 binds the tRNA-LC in the presence of NAD(P)H and converts RTCB-bound NAD(P)H into NAD(P) + , a typical oxidative co-enzyme. However, NAD(P) + here acts as an antioxidant and protects the tRNA-LC from oxidative inactivation, which is dependent on copper ions. Genetic variants of PYROXD1 that cause human myopathies only partially support tRNA-LC activity. Thus, we establish the tRNA-LC as an oxidation-sensitive metalloenzyme, safeguarded by the flavoprotein PYROXD1 through an unexpected redox mechanism.


  • Organizational Affiliation

    Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1A [auth AAAA]505Homo sapiensMutation(s): 0 
Gene Names: PYROXD1
EC: 1.8.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WU10 (Homo sapiens)
Explore Q8WU10 
Go to UniProtKB:  Q8WU10
PHAROS:  Q8WU10
GTEx:  ENSG00000121350 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WU10
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth AAAA]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth AAAA]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.23α = 90
b = 101.23β = 90
c = 143.45γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description