6Q32

The structure of the Mo-insertase domain Cnx1E (variant S269DD274S) from Arabidopsis thaliana in complex with Moco-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

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This is version 1.2 of the entry. See complete history


Literature

Mechanism of molybdate insertion into pterin-based molybdenum cofactors.

Probst, C.Yang, J.Krausze, J.Hercher, T.W.Richers, C.P.Spatzal, T.Kc, K.Giles, L.J.Rees, D.C.Mendel, R.R.Kirk, M.L.Kruse, T.

(2021) Nat Chem 13: 758-765

  • DOI: https://doi.org/10.1038/s41557-021-00714-1
  • Primary Citation of Related Structures:  
    6Q32

  • PubMed Abstract: 

    The molybdenum cofactor (Moco) is found in the active site of numerous important enzymes that are critical to biological processes. The bidentate ligand that chelates molybdenum in Moco is the pyranopterin dithiolene (molybdopterin, MPT). However, neither the mechanism of molybdate insertion into MPT nor the structure of Moco prior to its insertion into pyranopterin molybdenum enzymes is known. Here, we report this final maturation step, where adenylated MPT (MPT-AMP) and molybdate are the substrates. X-ray crystallography of the Arabidopsis thaliana Mo-insertase variant Cnx1E S269D D274S identified adenylated Moco (Moco-AMP) as an unexpected intermediate in this reaction sequence. X-ray absorption spectroscopy revealed the first coordination sphere geometry of Moco trapped in the Cnx1E active site. We have used this structural information to deduce a mechanism for molybdate insertion into MPT-AMP. Given their high degree of structural and sequence similarity, we suggest that this mechanism is employed by all eukaryotic Mo-insertases.


  • Organizational Affiliation

    Institute of Plant Biology, Technische Universität Braunschweig, Braunschweig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Molybdopterin biosynthesis protein CNX1471Arabidopsis thalianaMutation(s): 2 
Gene Names: CNX1At5g20990F22D1.6T10F18.20
EC: 2.10.1.1 (PDB Primary Data), 2.7.7.75 (PDB Primary Data)
UniProt
Find proteins for Q39054 (Arabidopsis thaliana)
Explore Q39054 
Go to UniProtKB:  Q39054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39054
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.01α = 90
b = 123.29β = 90
c = 133.14γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-02-17 
  • Deposition Author(s): Krausze, J.

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description