PDBsum entry 2woc

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Hydrolase PDB id
Protein chains
291 a.a. *
FMT ×3
GOL ×4
_MN ×6
_CL ×2
Waters ×372
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the dinitrogenase reductase-activating glycohydrolase (drag) from rhodospirillum rubrum
Structure: Adp-ribosyl-[dinitrogen reductase] glycohydrolase chain: a, b, c. Synonym: adp-ribosylglycohydrolase, dinitrogenase reductase-activating glycohydrolase. Engineered: yes
Source: Rhodospirillum rubrum. Organism_taxid: 1085. Strain: s1. Expressed in: escherichia coli. Expression_system_taxid: 469008.
2.20Å     R-factor:   0.177     R-free:   0.240
Authors: C.L.Berthold,H.Wang,S.Nordlund,M.Hogbom
Key ref:
C.L.Berthold et al. (2009). Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG. Proc Natl Acad Sci U S A, 106, 14247-14252. PubMed id: 19706507 DOI: 10.1073/pnas.0905906106
23-Jul-09     Release date:   11-Aug-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P14300  (DRAG_RHORU) -  ADP-ribosyl-[dinitrogen reductase] glycohydrolase
294 a.a.
291 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - ADP-ribosyl-[dinitrogen reductase] hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ADP-D-ribosyl-[dinitrogen reductase] = ADP-D-ribose + [dinitrogen reductase]
ADP-D-ribosyl-[dinitrogen reductase]
= ADP-D-ribose
+ [dinitrogen reductase]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nitrogen fixation   2 terms 
  Biochemical function     hydrolase activity     2 terms  


DOI no: 10.1073/pnas.0905906106 Proc Natl Acad Sci U S A 106:14247-14252 (2009)
PubMed id: 19706507  
Mechanism of ADP-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-ADP-ribosylhydrolase DraG.
C.L.Berthold, H.Wang, S.Nordlund, M.Högbom.
ADP-ribosylation is a ubiquitous regulatory posttranslational modification involved in numerous key processes such as DNA repair, transcription, cell differentiation, apoptosis, and the pathogenic mechanism of certain bacterial toxins. Despite the importance of this reversible process, very little is known about the structure and mechanism of the hydrolases that catalyze removal of the ADP-ribose moiety. In the phototrophic bacterium Rhodospirillum rubrum, dinitrogenase reductase-activating glycohydrolase (DraG), a dimanganese enzyme that reversibly associates with the cell membrane, is a key player in the regulation of nitrogenase activity. DraG has long served as a model protein for ADP-ribosylhydrolases. Here, we present the crystal structure of DraG in the holo and ADP-ribose bound forms. We also present the structure of a reaction intermediate analogue and propose a detailed catalytic mechanism for protein de-ADP-ribosylation involving ring opening of the substrate ribose. In addition, the particular manganese coordination in DraG suggests a rationale for the enzyme's preference for manganese over magnesium, although not requiring a redox active metal for the reaction.
  Selected figure(s)  
Figure 3.
Complex structures of DraG. (A) The reaction intermediate analogue structure with ADP-ribosyllysine on the surface of one DraG monomer reaching into the active site of another monomer. Inset: Amino acids with side chains involved in the binding site displayed as sticks. (B) 2Fo-Fc map for the ADP-ribosyllysine contoured at 1.0 σ. (C) 2Fo-Fc map for ADP-ribose in the D97N variant structure contoured at 1.0 σ. (D) Stereoview of the superimposed open ADP-ribosyllysine (yellow) and closed α-ADP-ribose (gray) in the active site. Interacting amino acids are shown in stick representation in dark green with red dashed bonds for the ADP-ribosyllysine complex structure and in pink with gray dashed bonds for the ADP-ribose D97N complex structure. Mn[A] is shown in magenta. Ribose atoms are labeled in black for the closed ribose and in red for the open conformation.
Figure 5.
Proposed catalytic mechanism for DraG. Amino acids actively participating in the reaction mechanism and manganese ions are displayed in gray. The circled Arg represents the ADP-ribosylated arginine in the modified protein. Dashed lines indicate hydrogen bonds and gray lines show metal coordination.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21267492 M.Högbom (2011).
Metal use in ribonucleotide reductase R2, di-iron, di-manganese and heterodinuclear--an intricate bioinorganic workaround to use different metals for the same reaction.
  Metallomics, 3, 110-120.  
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