› 4lr9

X-ray diffraction
2.1Å resolution

Phosphopentomutase S154A variant soaked with 2,3-dideoxyribose 5-phosphate

Released:
DOI: 10.2210/pdb4lr9/pdb
PDB entry 4lr9 coloured by chain, front view.
PDB entry 4lr9 coloured by chain, side view.
PDB entry 4lr9 coloured by chain, top view.
Source organism: Bacillus cereus
Primary publication:
Bioretrosynthetic construction of a didanosine biosynthetic pathway.
Birmingham WR, Starbird CA, Panosian TD, Nannemann DP, Iverson TM, Bachmann BO
Nat Chem Biol 10 392-9 (2014)
PMID: 24657930

Function and Biology Details

Reaction catalysed: 
Alpha-D-ribose 1-phosphate = D-ribose 5-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182450 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphopentomutase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 416 amino acids
Theoretical weight: 46.46 KDa
Source organism: Bacillus cereus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q818Z9 (Residues: 2-394; Coverage: 100%)
Gene names: BC_4087, deoB
Sequence domains: Metalloenzyme superfamily
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MN 10 x MN
Ligand GOL 2 x GOL
Ligand 1X4 1 x 1X4
1 modified residue:
Ligand TPO 3 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P21
Unit cell:
a: 92.329Å b: 76.615Å c: 107.236Å
α: 90° β: 108.96° γ: 90°
R-values:
R R work R free
0.171 0.169 0.213
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

16 review citations

Synthetic metabolism: metabolic engineering meets enzyme design.
Erb et al. (2017)
15 more

1 mention without citation

Bioretrosynthetic construction of a didanosine biosynthetic pathway.
Birmingham et al. (2014)