› 5isy

X-ray diffraction
2.35Å resolution

Crystal structure of Nudix family protein with NAD

Released:
DOI: 10.2210/pdb5isy/pdb
PDB entry 5isy coloured by chain, front view.
PDB entry 5isy coloured by chain, side view.
PDB entry 5isy coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural basis of prokaryotic NAD-RNA decapping by NudC.
Zhang D, Liu Y, Wang Q, Guan Z, Wang J, Liu J, Zou T, Yin P
OpenAccess logo Cell Res 26 1062-6 (2016)
PMID: 27561816

Function and Biology Details

Reaction catalysed: 
NAD(H) + H(2)O = AMP + NMN(H)
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-152424 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
NAD-capped RNA hydrolase NudC Chains: A, C
Molecule details ›
Chains: A, C
Length: 259 amino acids
Theoretical weight: 29.93 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32664 (Residues: 1-257; Coverage: 100%)
Gene names: JW5548, b3996, nudC, yjaD
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand NAD 2 x NAD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 52.411Å b: 98.702Å c: 113.739Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.182 0.244
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Regulation of mRNA Stability During Bacterial Stress Responses.
Vargas-Blanco et al. (2020)
5 more

3 mentions without citation

Structural basis of prokaryotic NAD-RNA decapping by NudC.
Zhang et al. (2016)
2 more