› 5d3z

X-ray diffraction
2.1Å resolution

Crystal structure of the thioesterase domain of deoxyerythronolide B synthase in complex with a small phosphonate inhibitor

Released:
DOI: 10.2210/pdb5d3z/pdb
PDB entry 5d3z coloured by chain, front view.
PDB entry 5d3z coloured by chain, side view.
PDB entry 5d3z coloured by chain, top view.
Source organism: Saccharopolyspora erythraea
Primary publication:
Towards a characterization of the structural determinants of specificity in the macrocyclizing thioesterase for deoxyerythronolide B biosynthesis.
Argyropoulos P, Bergeret F, Pardin C, Reimer JM, Pinto A, Boddy CN, Schmeing TM
Biochim Biophys Acta 1860 486-97 (2016)
PMID: 26592346

Function and Biology Details

Reaction catalysed: 
Propanoyl-CoA + 6 (2S)-methylmalonyl-CoA + 6 NADPH = 6-deoxyerythronolide B + 7 CoA + 6 CO(2) + H(2)O + 6 NADP(+)
Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169842 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 Chain: A
Molecule details ›
Chain: A
Length: 269 amino acids
Theoretical weight: 28.78 KDa
Source organism: Saccharopolyspora erythraea
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q03133 (Residues: 2904-3172; Coverage: 9%)
Gene name: eryA
Sequence domains: Thioesterase domain
Structure domains: alpha/beta hydrolase

Ligands and Environments

3 bound ligands:
Ligand 57H 1 x 57H
Ligand 1PE 1 x 1PE
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P321
Unit cell:
a: 112.544Å b: 112.544Å c: 42.78Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.171 0.17 0.19
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Trapping interactions between catalytic domains and carrier proteins of modular biosynthetic enzymes with chemical probes.
Gulick et al. (2018)
2 more

1 mention without citation

Thioesterase enzyme families: Functions, structures, and mechanisms.
Caswell et al. (2022)