Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.81 kDa 
• Atom Count: 2896 
• Modelled Residue Count: 339 
• Deposited Residue Count: 347 
• Unique protein chains: 1

2FOZ

human ADP-ribosylhydrolase 3

• PDB DOI: 10.2210/pdb2FOZ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-01-15 Released: 2006-10-10 
• Deposition Author(s): Mueller-Dieckmann, C., Weiss, M.S., Koch-Nolte, F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.209 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 

Literature

The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation.

Mueller-Dieckmann, C., Kernstock, S., Lisurek, M., von Kries, J.P., Haag, F., Weiss, M.S., Koch-Nolte, F.

(2006) Proc Natl Acad Sci U S A 103: 15026-15031

• PubMed: 17015823 
• DOI: 10.1073/pnas.0606762103
• Primary Citation of Related Structures:  
  2FOZ, 2FP0


• PubMed Abstract: 
  

Posttranslational modifications are used by cells from all kingdoms of life to control enzymatic activity and to regulate protein function. For many cellular processes, including DNA repair, spindle function, and apoptosis, reversible mono- and polyADP-ribosylation constitutes a very important regulatory mechanism. Moreover, many pathogenic bacteria secrete toxins which ADP-ribosylate human proteins, causing diseases such as whooping cough, cholera, and diphtheria. Whereas the 3D structures of numerous ADP-ribosylating toxins and related mammalian enzymes have been elucidated, virtually nothing is known about the structure of protein de-ADP-ribosylating enzymes. Here, we report the 3Dstructure of human ADP-ribosylhydrolase 3 (hARH3). The molecular architecture of hARH3 constitutes the archetype of an all-alpha-helical protein fold and provides insights into the reversibility of protein ADP-ribosylation. Two magnesium ions flanked by highly conserved amino acids pinpoint the active-site crevice. Recombinant hARH3 binds free ADP-ribose with micromolar affinity and efficiently de-ADP-ribosylates poly- but not monoADP-ribosylated proteins. Docking experiments indicate a possible binding mode for ADP-ribose polymers and suggest a reaction mechanism. Our results underscore the importance of endogenous ADP-ribosylation cycles and provide a basis for structure-based design of ADP-ribosylhydrolase inhibitors.

---

Organizational Affiliation: 

European Molecular Biology Laboratory Hamburg Outstation, c/o Deutsches Elektronen-Synchrotron, Institute of Immunology, University Hospital, Hamburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylhydrolase like 2	A	347	Homo sapiens	Mutation(s): 0  Gene Names: ADPRS, ADPRHL2, ARH3 EC: 3.5.1 (UniProt), 3.2.1.143 (UniProt), 3.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX46 (Homo sapiens) Explore Q9NX46  Go to UniProtKB:  Q9NX46
PHAROS:  Q9NX46 GTEx:  ENSG00000116863

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.209 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.3	α = 90
b = 60.4	β = 90
c = 97.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-15 
• Released Date: 2006-10-10 
Deposition Author(s): Mueller-Dieckmann, C., Weiss, M.S., Koch-Nolte, F.

Revision History  

• Version 1.0: 2006-10-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance