6IV5

Crystal structure of arabidopsis N6-mAMP deaminase MAPDA

• PDB DOI: https://doi.org/10.2210/pdb6IV5/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-02 Released: 2019-02-27 
• Deposition Author(s): Wu, B.X., Zhang, D., Nie, H.B., Shen, S.L., Li, S.S., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Structure ofArabidopsis thaliana N6-methyl-AMP deaminase ADAL with bound GMP and IMP and implications forN6-methyl-AMP recognition and processing.

Wu, B., Zhang, D., Nie, H., Shen, S., Li, Y., Li, S.

(2019) RNA Biol 16: 1504-1512

• PubMed: 31318636 
• DOI: https://doi.org/10.1080/15476286.2019.1642712
• Primary Citation of Related Structures:  
  6IV5, 6J23, 6J4T


• PubMed Abstract: 
  

  Arabidopsis thaliana aminohydrolase ( At ADAL) has been shown to be involved in the metabolism of N ⁶ -methyl-AMP, a proposed intermediate during m ⁶ A-modified RNA metabolism, which can be subsequently incorporated into newly synthesized RNA by Pol II. It has been proposed that At ADAL will prevent N ⁶ -methyl-AMP reuse and catabolize it to inosine monophosphate (IMP). Here, we have solved the crystal structures of At ADAL in the apo form and in complex with GMP and IMP in the presence of Zn ²⁺ . We have identified the substrate-binding pocket of At ADAL and compared it with that for adenosine deaminase (ADA), adenine deaminase (ADE) and AMP deaminase (AMPD) from multiple species. The comparisons reveal that plant ADAL1 may have the potential ability to catalyze different alkyl-group substituted substrates.

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Organizational Affiliation: 

Department of Biology, Southern University of Science and Technology , Shenzhen , Guangdong , China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 40.16 kDa 
• Atom Count: 2,795 
• Modelled Residue Count: 334 
• Deposited Residue Count: 355 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine/AMP deaminase family protein	A	355	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At4g04880, T4B21.20, T4B21_20 EC: 3.5.4
UniProt
Find proteins for Q8LPL7 (Arabidopsis thaliana) Explore Q8LPL7  Go to UniProtKB:  Q8LPL7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.904	α = 90
b = 82.352	β = 90
c = 86.686	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Wu, B.X., Zhang, D., Nie, H.B., Shen, S.L., Li, S.S., Patel, D.J.

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-07-31
  Changes: Data collection, Database references
• Version 1.2: 2019-09-11
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description