3G9D | pdb_00003g9d

Crystal structure glycohydrolase

• PDB DOI: https://doi.org/10.2210/pdb3G9D/pdb

• Classification: HYDROLASE
• Organism(s): Azospirillum brasilense
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-13 Released: 2009-07-14 
• Deposition Author(s): Li, X.-D., Winkler, F.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.266 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Dinitrogenase Reductase-activating Glycohydrolase (DRAG) Reveals Conservation in the ADP-Ribosylhydrolase Fold and Specific Features in the ADP-Ribose-binding Pocket

Li, X.-D., Huergo, L.F., Gasperina, A., Pedrosa, F.O., Merrick, M., Winkler, F.K.

(2009) J Mol Biology 390: 737-746

• PubMed: 19477184 
• DOI: https://doi.org/10.1016/j.jmb.2009.05.031
• Primary Citation Related Structures: 
  3G9D


• PubMed Abstract: 
  

  Protein-reversible ADP-ribosylation is emerging as an important post-translational modification used to control enzymatic and protein activity in different biological systems. This modification regulates nitrogenase activity in several nitrogen-fixing bacterial species. ADP-ribosylation is catalyzed by ADP-ribosyltransferases and is reversed by ADP-ribosylhydrolases. The structure of the ADP-ribosylhydrolase that acts on Azospirillum brasilense nitrogenase (dinitrogenase reductase-activating glycohydrolase, DraG) has been solved at a resolution of 2.5 A. This bacterial member of the ADP-ribosylhydrolase family acts specifically towards a mono-ADP-ribosylated substrate. The protein shows an all-alpha-helix structure with two magnesium ions located in the active site. Comparison of the DraG structure with orthologues deposited in the Protein Data Bank from Archaea and mammals indicates that the ADP-ribosylhydrolase fold is conserved in all domains of life. Modeling of the binding of the substrate ADP-ribosyl moiety to DraG is in excellent agreement with biochemical data.

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Organizational Affiliation: 
• Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.98 kDa 
• Atom Count: 4,518 
• Modeled Residue Count: 580 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dinitrogenase reductase activating glucohydrolase	A, B	297	Azospirillum brasilense	Mutation(s): 0  Gene Names: draG EC: 3.2.2.24
UniProt
Find proteins for A7XNI2 (Azospirillum brasilense) Explore A7XNI2  Go to UniProtKB:  A7XNI2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.266 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.866	α = 90
b = 163.866	β = 90
c = 46.274	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASES	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Li, X.-D., Winkler, F.K.

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description