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X-ray diffraction
2.25Å resolution

Crystal Structure of the dinitrogenase reductase-activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP- ribsoyllysine

Released:
DOI: 10.2210/pdb2wod/pdb
PDB entry 2wod coloured by chain, front view.
PDB entry 2wod coloured by chain, side view.
PDB entry 2wod coloured by chain, top view.
Source organism: Rhodospirillum rubrum
Primary publication:
Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG.
Berthold CL, Wang H, Nordlund S, Högbom M
Proc Natl Acad Sci U S A 106 14247-52 (2009)
PMID: 19706507

Function and Biology Details

Reaction catalysed: 
[Dinitrogen reductase]-N(omega)-alpha-(ADP-D-ribosyl)-L-arginine = ADP-D-ribose + [dinitrogen reductase]-L-arginine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146899 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ADP-ribosyl-[dinitrogen reductase] glycohydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 299 amino acids
Theoretical weight: 32.24 KDa
Source organism: Rhodospirillum rubrum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P14300 (Residues: 1-294; Coverage: 100%)
Gene name: draG
Sequence domains: ADP-ribosylglycohydrolase
Structure domains: ADP-ribosylation/Crystallin J1

Ligands and Environments

4 bound ligands:
Ligand MN 2 x MN
Ligand ZZC 2 x ZZC
Ligand CL 1 x CL
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: P3121
Unit cell:
a: 77.306Å b: 77.306Å c: 245.593Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.197 0.242
Expression system: Escherichia coli BL21(DE3)

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Citations

9 review citations

Structures and Mechanisms of Enzymes Employed in the Synthesis and Degradation of PARP-Dependent Protein ADP-Ribosylation.
Barkauskaite et al. (2015)
8 more

4 mentions without citation

Structural biology of the writers, readers, and erasers in mono- and poly(ADP-ribose) mediated signaling.
Karlberg et al. (2013)
3 more