4FL0 | pdb_00004fl0

Crystal structure of ALD1 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb4FL0/pdb

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


• Deposited: 2012-06-14 Released: 2013-02-20 
• Deposition Author(s): Sobolev, V., Edelman, M., Dym, O., Unger, T., Albeck, S., Kirma, M., Galili, G., Israel Structural Proteomics Center (ISPC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Structure of ALD1, a plant-specific homologue of the universal diaminopimelate aminotransferase enzyme of lysine biosynthesis.

Sobolev, V., Edelman, M., Dym, O., Unger, T., Albeck, S., Kirma, M., Galili, G.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 84-89

• PubMed: 23385743 
• DOI: https://doi.org/10.1107/S1744309112050270
• Primary Citation Related Structures: 
  4FL0


• PubMed Abstract: 
  

  Diaminopimelate aminotransferase (DAP-AT) is an enzyme in the lysine-biosynthesis pathway. Conversely, ALD1, a close homologue of DAP-AT in plants, uses lysine as a substrate in vitro. Both proteins require pyridoxal-5'-phosphate (PLP) for their activity. The structure of ALD1 from the flowering plant Arabidopsis thaliana (AtALD1) was solved at a resolution of 2.3 Å. Comparison of AtALD1 with the previously solved structure of A. thaliana DAP-AT (AtDAP-AT) revealed similar interactions with PLP despite sequence differences within the PLP-binding site. However, sequence differences between the binding site of AtDAP-AT for malate, a purported mimic of substrate binding, and the corresponding site in AtALD1 led to different interactions. This suggests that either the substrate itself, or the substrate-binding mode, differs in the two proteins, supporting the known in vitro findings.

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Organizational Affiliation: 
• Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel. [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)

Macromolecule Content 

• Total Structure Weight: 101.76 kDa 
• Atom Count: 6,368 
• Modeled Residue Count: 815 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase ALD1	A, B	456	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ALD1, At2g13810, F13J11.16 EC: 2.6.1
UniProt
Find proteins for Q9ZQI7 (Arabidopsis thaliana) Explore Q9ZQI7  Go to UniProtKB:  Q9ZQI7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.28	α = 90
b = 89.87	β = 90
c = 180.7	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Sobolev, V., Edelman, M., Dym, O., Unger, T., Albeck, S., Kirma, M., Galili, G., Israel Structural Proteomics Center (ISPC)

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description