› 6qkb

X-ray diffraction
1.7Å resolution

Crystal structure of the beta-hydroxyaspartate aldolase of Paracoccus denitrificans

Released:
DOI: 10.2210/pdb6qkb/pdb
PDB entry 6qkb coloured by chain, front view.
PDB entry 6qkb coloured by chain, side view.
PDB entry 6qkb coloured by chain, top view.
Source organism: Paracoccus denitrificans
Primary publication:
Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle.
Schada von Borzyskowski L, Severi F, Krüger K, Hermann L, Gilardet A, Sippel F, Pommerenke B, Claus P, Cortina NS, Glatter T, Zauner S, Zarzycki J, Fuchs BM, Bremer E, Maier UG, Amann RI, Erb TJ
Nature 575 500-504 (2019)
PMID: 31723261

Function and Biology Details

Reaction catalysed: 
D-erythro-3-hydroxyaspartate = glycine + glyoxylate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106570 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-hydroxy-D-aspartate aldolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 387 amino acids
Theoretical weight: 41.84 KDa
Source organism: Paracoccus denitrificans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A1B8Z1 (Residues: 1-387; Coverage: 100%)
Gene names: Pden_3919, bhcC
Sequence domains:

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P212121
Unit cell:
a: 66.598Å b: 75.247Å c: 157.31Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.158 0.176
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

TCA Cycle Replenishing Pathways in Photosynthetic Purple Non-Sulfur Bacteria Growing with Acetate.
Petushkova et al. (2021)
3 more