› 2po3

X-ray diffraction
2.1Å resolution

Crystal Structure Analysis of DesI in the presence of its TDP-sugar product

Released:
DOI: 10.2210/pdb2po3/pdb
Model geometry
Fit model/data
PDB entry 2po3 coloured by chain, front view.
PDB entry 2po3 coloured by chain, side view.
PDB entry 2po3 coloured by chain, top view.
Source organism: Streptomyces venezuelae
Primary publication:
Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine.
Burgie ES, Holden HM
Biochemistry 46 8999-9006 (2007)
PMID: 17630700

Function and Biology Details

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-195641 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-dehydrase Chains: A, B
Molecule details ›
Chains: A, B
Length: 424 amino acids
Theoretical weight: 45.48 KDa
Source organism: Streptomyces venezuelae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9ZGH0 (Residues: 1-415; Coverage: 100%)
Gene name: desI
Sequence domains: DegT/DnrJ/EryC1/StrS aminotransferase family
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand T4K 2 x T4K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 59.5Å b: 66.8Å c: 242Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.18 0.248
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Natural-product sugar biosynthesis and enzymatic glycodiversification.
Thibodeaux et al. (2008)
6 more

9 mentions without citation

The structural biology of enzymes involved in natural product glycosylation.
Singh et al. (2012)
8 more

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO