› 6vck

X-ray diffraction
2.69Å resolution

Crystal structure of E.coli RppH-DapF in complex with GDP, Mg2+ and F-

Released:
DOI: 10.2210/pdb6vck/pdb
PDB entry 6vck coloured by chain, front view.
PDB entry 6vck coloured by chain, side view.
PDB entry 6vck coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Gao A, Vasilyev N, Kaushik A, Duan W, Serganov A
Nucleic Acids Res 48 3776-3788 (2020)
PMID: 31960065

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: 275 amino acids
Theoretical weight: 30.15 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
RNA pyrophosphohydrolase Chain: B
Molecule details ›
Chain: B
Length: 161 amino acids
Theoretical weight: 18.97 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A776 (Residues: 1-160; Coverage: 91%)
Gene names: JW2798, b2830, nudH, rppH, ygdP
Sequence domains: NUDIX domain

Ligands and Environments

4 bound ligands:
Ligand MG 3 x MG
Ligand GDP 1 x GDP
Ligand CL 1 x CL
Ligand F 1 x F
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2221
Unit cell:
a: 161.84Å b: 193.601Å c: 51.037Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.226 0.268
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

The stringent response and physiological roles of (pp)pGpp in bacteria.
Irving et al. (2021)
3 other articles

1 mention without citation

Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Gao et al. (2020)