Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.07 kDa 
• Atom Count: 2639 
• Residue Count: 292 
• Unique protein chains: 1

1Q33

Crystal structure of human ADP-ribose pyrophosphatase NUDT9

• DOI: 10.2210/pdb1Q33/pdb

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


• Deposited: 2003-07-28 Released: 2003-09-30 
• Deposition Author(s): Shen, B.W., Perraud, A.L., Scharenberg, A., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.231 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

The Crystal Structure and Mutational Analysis of Human NUDT9

Shen, B.W., Perraud, A.L., Scharenberg, A., Stoddard, B.L.

(2003) J Mol Biol 332: 385-398

• PubMed: 12948489 
• DOI: 10.1016/s0022-2836(03)00954-9
• Primary Citation of Related Structures:  
  1QVJ, 1Q33


• PubMed Abstract: 
  

Human ADP-ribose pyrophosphatase NUDT9 belongs to a superfamily of Nudix hydrolases that catabolize potentially toxic compounds in the cell. The enzyme hydrolyzes ADP-ribose (ADPR) to AMP and ribose 5'-phosphate. NUDT9 shares 39% sequence identity with the C-terminal cytoplasmic domain of the ADPR-gated calcium channel TRPM2, which exhibits low but specific enzyme activity. We determined crystal structures of NUDT9 in the presence and in the absence of the reaction product ribose 5'-phosphate. On the basis of these structures and comparison with a bacterial homologue, a model of the substrate complex was built. The structure and activity of a double point mutant (R(229)E(230)F(231) to R(229)I(230)L(231)), which mimics the Nudix signature of the ion channel domain, was determined. Finally, the activities of a pair of additional mutated constructs were compared to the wild-type enzyme. The first corresponds to a minimal Nudix domain missing an N-terminal domain and C-terminal tail; the second disrupts two potential general bases in the active site. NUDT9 contains an N-terminal domain with a novel fold and a catalytic C-terminal Nudix domain. Unlike its closest functional homologue (homodimeric Escherichia coli ADPRase), it is active as a monomer, and the substrate is bound in a cleft between the domains. The structure of the RIL mutant provides structural basis for the reduced activity of the TRPM2 ion channel. The conformation and binding interactions of ADPR substrate are predicted to differ from those observed for E.coli ADPRase; mutation of structurally aligned acidic residues in their active sites produce significantly different effects on catalytic efficiency, indicating that their reaction pathways and mechanisms may have diverged.

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Organizational Affiliation: 

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribose pyrophosphatase	A	292	Homo sapiens	Mutation(s): 0  Gene Names: NUDT9, NUDT10, PSEC0099, UNQ3012/PRO9771 EC: 3.6.1.13
Find proteins for Q9BW91 (Homo sapiens) Explore Q9BW91  Go to UniProtKB:  Q9BW91
NIH Common Fund Data Resources
PHAROS:  Q9BW91 GTEx:  ENSG00000170502

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	A	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.231 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.837	α = 90
b = 87.497	β = 90
c = 119.814	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-28 
• Released Date: 2003-09-30 
Deposition Author(s): Shen, B.W., Perraud, A.L., Scharenberg, A., Stoddard, B.L.

Revision History 

• Version 1.0: 2003-09-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary