7YQA

Crystal structure of D-threonine aldolase from Chlamydomonas reinhardtii

• PDB DOI: https://doi.org/10.2210/pdb7YQA/pdb

• Classification: LYASE
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-08-05 Released: 2023-02-15 
• Deposition Author(s): Hirato, Y., Goto, M., Mizobuchi, T., Muramatsu, H., Tanigawa, M., Nishimura, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.249 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

Structure of pyridoxal 5'-phosphate-bound D-threonine aldolase from Chlamydomonas reinhardtii.

Hirato, Y., Goto, M., Mizobuchi, T., Muramatsu, H., Tanigawa, M., Nishimura, K.

(2023) Acta Crystallogr F Struct Biol Commun 79: 31-37

• PubMed: 36748339 
• DOI: https://doi.org/10.1107/S2053230X23000304
• Primary Citation of Related Structures:  
  7YQA


• PubMed Abstract: 
  

  D-Threonine aldolase (DTA) is a pyridoxal-5'-phosphate-dependent enzyme which catalyzes the reversible aldol reaction of glycine with a corresponding aldehyde to yield the D-form β-hydroxy-α-amino acid. This study produced and investigated the crystal structure of DTA from Chlamydomonas reinhardtii (CrDTA) at 1.85 Å resolution. To our knowledge, this is the first report on the crystal structure of eukaryotic DTA. Compared with the structure of bacterial DTA, CrDTA has a similar arrangement of active-site residues. On the other hand, we speculated that some non-conserved residues alter the affinity for substrates and inhibitors. The structure of CrDTA could provide insights into the structural framework for structure-guided protein engineering studies to modify reaction selectivity.

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Organizational Affiliation: 

Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.

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: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 181.5 kDa 
• Atom Count: 12,435 
• Modelled Residue Count: 1,584 
• Deposited Residue Count: 1,712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-threonine aldolase	A, B, C, D	428	Chlamydomonas reinhardtii	Mutation(s): 0  EC: 4.1.2.42
UniProt
Find proteins for A0A1C9ZZ39 (Chlamydomonas reinhardtii) Explore A0A1C9ZZ39  Go to UniProtKB:  A0A1C9ZZ39

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.249 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.792	α = 77.07
b = 74.096	β = 69.34
c = 89.939	γ = 71.93

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Hirato, Y., Goto, M., Mizobuchi, T., Muramatsu, H., Tanigawa, M., Nishimura, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description