4F0D

Human ARTD15/PARP16 IN COMPLEX WITH 3-AMINOBENZAMIDE

• PDB DOI: https://doi.org/10.2210/pdb4F0D/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-04 Released: 2012-06-13 
• Deposition Author(s): Karlberg, T., Thorsell, A.G., Kallas, A., Schuler, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.287 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 

Literature

Crystal Structure of Human ADP-ribose Transferase ARTD15/PARP16 Reveals a Novel Putative Regulatory Domain.

Karlberg, T., Thorsell, A.G., Kallas, A., Schuler, H.

(2012) J Biol Chem 287: 24077-24081

• PubMed: 22661712 
• DOI: https://doi.org/10.1074/jbc.M112.379289
• Primary Citation of Related Structures:  
  4F0D


• PubMed Abstract: 
  

  ADP-ribosylation is involved in the regulation of DNA repair, transcription, and other processes. The 18 human ADP-ribose transferases with diphtheria toxin homology include ARTD1/PARP1, a cancer drug target. Knowledge of other family members may guide therapeutics development and help evaluate potential drug side effects. Here, we present the crystal structure of human ARTD15/PARP16, a previously uncharacterized enzyme. ARTD15 features an α-helical domain that packs against its transferase domain without making direct contact with the NAD(+)-binding crevice or the donor loop. Thus, this novel domain does not resemble the regulatory domain of ARTD1. ARTD15 displays auto-mono(ADP-ribosylation) activity and is affected by canonical poly(ADP-ribose) polymerase inhibitors. These results add to a framework that will facilitate research on a medically important family of enzymes.

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Organizational Affiliation: 

Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.36 kDa 
• Atom Count: 3,067 
• Modelled Residue Count: 405 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 16	A, B	277	Homo sapiens	Mutation(s): 0  Gene Names: C15orf30, PARP16 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5Y8 (Homo sapiens) Explore Q8N5Y8  Go to UniProtKB:  Q8N5Y8
PHAROS:  Q8N5Y8 GTEx:  ENSG00000138617

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3AB	C [auth A]	3-aminobenzamide C7 H8 N2 O GSCPDZHWVNUUFI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.287 
• R-Value Work: 0.246 
• R-Value Observed: 0.248 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.824	α = 90
b = 195.349	β = 90
c = 60.412	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
autoSHARP	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Karlberg, T., Thorsell, A.G., Kallas, A., Schuler, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2012-08-15
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations