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PDBsum entry 2woe

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2woe
Jmol
Contents
Protein chains
291 a.a. *
Ligands
AR6 ×3
TLA
GOL
Metals
_MN ×3
Waters ×758
* Residue conservation analysis
PDB id:
2woe
Name: Hydrolase
Title: Crystal structure of the d97n variant of dinitrogenase reductase-activating glycohydrolase (drag) from rhodospirillum rubrum in complex with adp-ribose
Structure: Adp-ribosyl-[dinitrogen reductase] glycohydrolase chain: a, b, c. Synonym: dinitrogenase reductase-activating glycohydrolas, eadp-ribosylglycohydrolase. Engineered: yes. Mutation: yes
Source: Rhodospirillum rubrum. Organism_taxid: 1085. Strain: s1. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.169     R-free:   0.207
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
Date:
23-Jul-09     Release date:   18-Aug-09    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14300  (DRAG_RHORU) -  ADP-ribosyl-[dinitrogen reductase] glycohydrolase
Seq:
Struc:
294 a.a.
291 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.2.24  - 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
Bound ligand (Het Group name = AR6)
corresponds exactly
+ [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  

 

 
    reference    
 
 
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.
 
  ABSTRACT  
 
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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.