› 7ub8

X-ray diffraction
2.3Å resolution

The crystal structure of the K38A/K137A/K233A/K234A quadruple mutant of E. coli YGGS in complex with PLP

Released:
DOI: 10.2210/pdb7ub8/pdb
PDB entry 7ub8 coloured by chain, front view.
PDB entry 7ub8 coloured by chain, side view.
PDB entry 7ub8 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Characterization of the Escherichia coli pyridoxal 5'-phosphate homeostasis protein (YggS): role of lysine residues in PLP binding and protein stability.
Tramonti A, Ghatge MS, Babor JT, Musayev FN, di Salvo ML, Barile A, Colotti G, Giorgi A, Paredes SD, Donkor AK, Al Mughram MH, de Crécy-Lagard V, Safo MK, Contestabile R
Protein Sci e4471 (2022)
PMID: 36218140

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159198 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxal phosphate homeostasis protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 234 amino acids
Theoretical weight: 25.59 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P67080 (Residues: 1-234; Coverage: 100%)
Gene names: JW2918, b2951, yggS
Sequence domains: Alanine racemase, N-terminal domain

Ligands and Environments

2 bound ligands:
Ligand PLP 2 x PLP
Ligand BU1 3 x BU1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P41212
Unit cell:
a: 129.646Å b: 129.646Å c: 76.911Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.186 0.232
Expression system: Escherichia coli

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Citations

3 citation in other articles

Mechanistic insights into sulfur source-driven physiological responses and metabolic reorganization in the fuel-biodesulfurizing Rhodococcus qingshengii IGTS8.
Zumsteg et al. (2023)
2 more

2 mentions without citation

The Conserved Family of the Pyridoxal Phosphate-Binding Protein (PLPBP) and Its Cyanobacterial Paradigm PipY.
Tremiño et al. (2022)
1 more