› 1st0

X-ray diffraction
1.9Å resolution

Structure of DcpS bound to m7GpppG

Released:
DOI: 10.2210/pdb1st0/pdb
PDB entry 1st0 coloured by chain, front view.
PDB entry 1st0 coloured by chain, side view.
PDB entry 1st0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity.
Gu M, Fabrega C, Liu SW, Liu H, Kiledjian M, Lima CD
Mol Cell 14 67-80 (2004)
PMID: 15068804

Function and Biology Details

Reaction catalysed: 
A 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] + H(2)O = N(7)-methylguanosine 5'-phosphate + a 5'-diphospho-[mRNA]
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188399 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
m7GpppX diphosphatase Chains: A, B
Molecule details ›
Chains: A, B
Length: 337 amino acids
Theoretical weight: 38.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96C86 (Residues: 1-337; Coverage: 100%)
Gene names: DCPS, DCS1, HINT5, HSPC015
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand GTG 2 x GTG
Ligand YT3 3 x YT3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P212121
Unit cell:
a: 59.446Å b: 94.783Å c: 178.328Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.187 0.231
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Messenger RNA turnover in eukaryotes: pathways and enzymes.
Meyer et al. (2004)
10 more

7 mentions without citation

Applications of Phosphate Modification and Labeling to Study (m)RNA Caps.
Warminski et al. (2017)
6 more