Crystal structure of human cytosolic 5'-nucleotidase III in complex with phosphate and magnesium

Experimental Data Snapshot

  • Resolution: 3.01 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.185 

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Crystal Structure of Human Cytosolic 5'-Nucleotidase II: Insights Into Allosteric Regulation and Substrate Recognition.

Wallden, K.Stenmark, P.Nyman, T.Flodin, S.Graslund, S.Loppnau, P.Bianchi, V.Nordlund, P.

(2007) J Biol Chem 282: 17828

  • DOI: https://doi.org/10.1074/jbc.M700917200
  • Primary Citation of Related Structures:  
    2CN1, 2J2C, 2JC9, 2JCM, 2JGA

  • PubMed Abstract: 

    Cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates and regulates the IMP and GMP pools within the cell. It possesses phosphotransferase activity and thereby also catalyzes the reverse reaction. Both reactions are allosterically activated by adenine-based nucleotides and 2,3-bisphosphoglycerate. We have solved structures of cytosolic 5'-nucleotidase II as native protein (2.2 Angstrom) and in complex with adenosine (1.5 Angstrom) and beryllium trifluoride (2.15 Angstrom) The tetrameric enzyme is structurally similar to enzymes of the haloacid dehalogenase (HAD) superfamily, including mitochondrial 5'(3')-deoxyribonucleotidase and cytosolic 5'-nucleotidase III but possesses additional regulatory regions that contain two allosteric effector sites. At effector site 1 located near a subunit interface we modeled diadenosine tetraphosphate with one adenosine moiety in each subunit. This efficiently glues the tetramer subunits together in pairs. The model shows why diadenosine tetraphosphate but not diadenosine triphosphate activates the enzyme and supports a role for cN-II during apoptosis when the level of diadenosine tetraphosphate increases. We have also modeled 2,3-bisphosphoglycerate in effector site 1 using one phosphate site from each subunit. By comparing the structure of cytosolic 5'-nucleotidase II with that of mitochondrial 5'(3')-deoxyribonucleotidase in complex with dGMP, we identified residues involved in substrate recognition.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOSOLIC 5'-NUCLEOTIDASE III292Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0P0 (Homo sapiens)
Explore Q9H0P0 
Go to UniProtKB:  Q9H0P0
GTEx:  ENSG00000122643 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0P0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.01 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.459α = 90
b = 101.036β = 90
c = 77.046γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description