Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 47.95 kDa 
• Atom Count: 3397 
• Modelled Residue Count: 390 
• Deposited Residue Count: 424 
• Unique protein chains: 1

2DSC

Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and ADP-ribose

• PDB DOI: 10.2210/pdb2DSC/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-06-28 Released: 2006-11-14 
• Deposition Author(s): Zha, M., Zhong, C., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Literature

Crystal Structures of Human NUDT5 Reveal Insights into the Structural Basis of the Substrate Specificity

Zha, M., Zhong, C., Peng, Y., Hu, H., Ding, J.

(2006) J Mol Biol 364: 1021-1033

• PubMed: 17052728 
• DOI: 10.1016/j.jmb.2006.09.078
• Primary Citation of Related Structures:  
  2DSB, 2DSC, 2DSD


• PubMed Abstract: 
  

Human NUDT5 (hNUDT5) is an ADP-ribose pyrophosphatase (ADPRase) belonging to the Nudix hydrolase superfamily. It presumably plays important roles in controlling the intracellular level of ADP-ribose (ADPR) to prevent non-enzymatic ADP-ribosylation by hydrolyzing ADPR to AMP and ribose 5'-phosphate. We report here the crystal structures of hNUDT5 in apo form, in complex with ADPR, and in complex with AMP with bound Mg2+. hNUDT5 forms a homodimer with substantial domain swapping and assumes a structure more similar to Escherichia coli ADPRase ORF209 than human ADPRase NUDT9. The adenine moiety of the substrates is specifically recognized by the enzyme via hydrogen-bonding interactions between N1 and N6 of the base and Glu47 of one subunit, and between N7 of the base and Arg51 of the other subunit, providing the molecular basis for the high selectivity of hNUDT5 for ADP-sugars over other sugar nucleotides. Structural comparisons with E. coli ADPRase ORF209 and ADPXase ORF186 indicate that the existence of an aromatic residue on loop L8 in ORF186 seems to be positively correlated with its enzymatic activity on APnA, whereas hNUDT5 and ORF209 contain no such residue and thus have low or no activities on APnA.

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Organizational Affiliation: 

State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-sugar pyrophosphatase	A, B	212	Homo sapiens	Mutation(s): 0  Gene Names: NUDT5, NUDIX5, HSPC115 EC: 3.6.1.13 (PDB Primary Data), 3.6.1 (PDB Primary Data), 3.6.1.58 (UniProt), 2.7.7.96 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKK9 (Homo sapiens) Explore Q9UKK9  Go to UniProtKB:  Q9UKK9
PHAROS:  Q9UKK9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APR	D [auth A], F [auth B]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.466	α = 90
b = 40.623	β = 121.44
c = 99.685	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-28 
• Released Date: 2006-11-14 
Deposition Author(s): Zha, M., Zhong, C., Ding, J.

Revision History  

• Version 1.0: 2006-11-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance