6GBC | pdb_00006gbc

The Structure of variant R369A of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP and molybdate

• PDB DOI: https://doi.org/10.2210/pdb6GBC/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-04-13 Released: 2018-07-18 
• Deposition Author(s): Krausze, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

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

• PubMed: 29717023 
• DOI: https://doi.org/10.1042/BCJ20170935
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Plant Biology, Braunschweig University of Technology, 38106 Braunschweig, Germany.
Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, U.S.A.
Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
Department for Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Braunschweig University of Technology, Spielmannstrasse 7, 38106 Braunschweig, Germany.
Department of Plant Biology, Braunschweig University of Technology, 38106 Braunschweig, Germany [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS, equilibrium centrifugation, gel filtration

Macromolecule Content 

• Total Structure Weight: 49.59 kDa 
• Atom Count: 3,572 
• Modeled Residue Count: 423 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdopterin biosynthesis protein CNX1	A	460	Arabidopsis thaliana	Mutation(s): 1  Gene Names: CNX1, At5g20990, F22D1.6, T10F18.20 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MOO (Subject of Investigation/LOI)	H [auth A]	MOLYBDATE ION Mo O4 MEFBJEMVZONFCJ-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.84	α = 90
b = 123.9	β = 90
c = 131.54	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing
Coot	model building
autoBUSTER	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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