6ETF

The Structure of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP and molybdate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The functional principle of eukaryotic molybdenum insertases.

Krausze, J.Hercher, T.W.Zwerschke, D.Kirk, M.L.Blankenfeldt, W.Mendel, R.R.Kruse, T.

(2018) Biochem J 475: 1739-1753

  • DOI: https://doi.org/10.1042/BCJ20170935
  • Primary Citation of Related Structures:  
    6ETD, 6ETF, 6ETH, 6GAX, 6GB0, 6GB4, 6GB9, 6GBC, 6GBF

  • PubMed Abstract: 

    The molybdenum cofactor (Moco) is a redox-active prosthetic group found in the active site of Moco-dependent enzymes, which are vitally important for life. Moco biosynthesis involves several enzymes that catalyze the subsequent conversion of GTP into cyclic pyranopterin monophosphate (cPMP), molybdopterin (MPT), adenylated MPT (MPT-AMP), and finally Moco. While the underlying principles of cPMP, MPT, and MPT-AMP formation are well understood, the molybdenum insertase (Mo-insertase)-catalyzed final Moco maturation step is not. In the present study, we analyzed high-resolution X-ray datasets of the plant Mo-insertase Cnx1E that revealed two molybdate-binding sites within the active site, hence improving the current view on Cnx1E functionality. The presence of molybdate anions in either of these sites is tied to a distinctive backbone conformation, which we suggest to be essential for Mo-insertase molybdate selectivity and insertion efficiency.


  • Organizational Affiliation

    Department for Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig University of Technology, Spielmannstrasse 7, 38106 Braunschweig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Molybdopterin biosynthesis protein CNX1471Arabidopsis thalianaMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
MOO (Subject of Investigation/LOI)
Query on MOO

Download Ideal Coordinates CCD File 
D [auth A]MOLYBDATE ION
Mo O4
MEFBJEMVZONFCJ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.11α = 90
b = 123.57β = 90
c = 131.79γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MxCuBEdata collection
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2018-07-18 
  • Deposition Author(s): Krausze, J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description