Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 95663.66 
• Atom Count: 6327 
• Residue Count: 864 
• Unique protein chains: 1

2Z1Z

Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana complexed with L-malate ion

• DOI: 10.2210/pdb2Z1Z/pdb

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


• Deposited: 2007-05-16 Released: 2007-07-17 
• Deposition Author(s): Watanabe, N., Cherney, M.M., van Belkum, M.J., Marcus, S.L., Flegel, M.D., Clay, M.D., Deyholos, M.K., Vederas, J.C., James, M.N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.251 
• R-Value Work: 0.180 

Literature

Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia

Watanabe, N., Cherney, M.M., van Belkum, M.J., Marcus, S.L., Flegel, M.D., Clay, M.D., Deyholos, M.K., Vederas, J.C., James, M.N.

(2007) J.Mol.Biol. 371: 685-702

• PubMed: 17583737 
• DOI: 10.1016/j.jmb.2007.05.061
• Primary Citation of Related Structures:  
  2Z20


• PubMed Abstract: 
  

The essential biosynthetic pathway to l-Lysine in bacteria and plants is an attractive target for the development of new antibiotics or herbicides because it is absent in humans, who must acquire this amino acid in their diet. Plants use a shortcut of a bacterial pathway to l-Lysine in which the pyridoxal-5'-phosphate (PLP)-dependent enzyme ll-diaminopimelate aminotransferase (LL-DAP-AT) transforms l-tetrahydrodipicolinic acid (L-THDP) directly to LL-DAP. In addition, LL-DAP-AT was recently found in Chlamydia sp., suggesting that inhibitors of this enzyme may also be effective against such organisms. In order to understand the mechanism of this enzyme and to assist in the design of inhibitors, the three-dimensional crystal structure of LL-DAP-AT was determined at 1.95 A resolution. The cDNA sequence of LL-DAP-AT from Arabidopsis thaliana (AtDAP-AT) was optimized for expression in bacteria and cloned in Escherichia coli without its leader sequence but with a C-terminal hexahistidine affinity tag to aid protein purification. The structure of AtDAP-AT was determined using the multiple-wavelength anomalous dispersion (MAD) method with a seleno-methionine derivative. AtDAP-AT is active as a homodimer with each subunit having PLP in the active site. It belongs to the family of type I fold PLP-dependent enzymes. Comparison of the active site residues of AtDAP-AT and aspartate aminotransferases revealed that the PLP binding residues in AtDAP-AT are well conserved in both enzymes. However, Glu97* and Asn309* in the active site of AtDAP-AT are not found at similar positions in aspartate aminotransferases, suggesting that specific substrate recognition may require these residues from the other monomer. A malate-bound structure of AtDAP-AT allowed LL-DAP and L-glutamate to be modelled into the active site. These initial three-dimensional structures of LL-DAP-AT provide insight into its substrate specificity and catalytic mechanism.

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Organizational Affiliation: 

Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LL-diaminopimelate aminotransferase	A, B	432	Arabidopsis thaliana	Mutation(s): 0  Gene Names: DAP (AGD2) EC: 2.6.1.83
Find proteins for Q93ZN9 (Arabidopsis thaliana) Go to Gene View: DAP Go to UniProtKB:  Q93ZN9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MLT	A	D-MALATE (2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
PLP	A, B	PYRIDOXAL-5'-PHOSPHATE VITAMIN B6 Phosphate C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.251 
• R-Value Work: 0.180 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 102.587	α = 90.00
b = 102.587	β = 90.00
c = 172.939	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-16 
• Released Date: 2007-07-17 
• Deposition Author(s): Watanabe, N., Cherney, M.M., van Belkum, M.J., Marcus, S.L., Flegel, M.D., Clay, M.D., Deyholos, M.K., Vederas, J.C., James, M.N.G.

Revision History 

• Version 1.0: 2007-07-17
  Type: Initial release
• Version 1.1: 2007-09-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance