› 5ygu

X-ray diffraction
2.3Å resolution

Crystal structure of Escherichia coli (strain K12) mRNA Decapping Complex RppH-DapF

Released:
DOI: 10.2210/pdb5ygu/pdb
PDB entry 5ygu coloured by chain, front view.
PDB entry 5ygu coloured by chain, side view.
PDB entry 5ygu coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli.
Wang Q, Zhang D, Guan Z, Li D, Pei K, Liu J, Zou T, Yin P
Nucleic Acids Res 46 6880-6892 (2018)
PMID: 29931175

Function and Biology Details

Reaction catalysed: 
LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141365 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Diaminopimelate epimerase Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 30.25 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A6K1 (Residues: 1-274; Coverage: 100%)
Gene names: JW5592, b3809, dapF
Sequence domains: Diaminopimelate epimerase
Structure domains: Diaminopimelate Epimerase; Chain A, domain 1
RNA pyrophosphohydrolase Chain: B
Molecule details ›
Chain: B
Length: 168 amino acids
Theoretical weight: 20.07 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A776 (Residues: 1-158; Coverage: 90%)
Gene names: JW2798, b2830, nudH, rppH, ygdP
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand TLA 1 x TLA
Ligand IOD 12 x IOD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P41212
Unit cell:
a: 86.418Å b: 86.418Å c: 173.093Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.239
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Noncanonical features and modifications on the 5'-end of bacterial sRNAs and mRNAs.
Vasilyev et al. (2019)
2 more

2 mentions without citation

DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli.
Wang et al. (2018)
1 more