3O1C

High resolution crystal structure of histidine triad nucleotide-binding protein 1 (Hint1) C38A mutant from rabbit complexed with Adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Histidine Triad Nucleotide-binding Protein 1 (HINT-1) Phosphoramidase Transforms Nucleoside 5'-O-Phosphorothioates to Nucleoside 5'-O-Phosphates.

Ozga, M.Dolot, R.Janicka, M.Kaczmarek, R.Krakowiak, A.

(2010) J.Biol.Chem. 285: 40809-40818

  • DOI: 10.1074/jbc.M110.162065
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleoside 5'-O-phosphorothioates are formed in vivo as primary products of hydrolysis of oligo(nucleoside phosphorothioate)s (PS-oligos) that are applied as antisense therapeutic molecules. The biodistribution of PS-oligos and their pharmacokinetics ...

    Nucleoside 5'-O-phosphorothioates are formed in vivo as primary products of hydrolysis of oligo(nucleoside phosphorothioate)s (PS-oligos) that are applied as antisense therapeutic molecules. The biodistribution of PS-oligos and their pharmacokinetics have been widely reported, but little is known about their subsequent decay inside the organism. We suggest that the enzyme responsible for nucleoside 5'-O-monophosphorothioate ((d)NMPS) metabolism could be histidine triad nucleotide-binding protein 1 (Hint-1), a phosphoramidase belonging to the histidine triad (HIT) superfamily that is present in all forms of life. An additional, but usually ignored, activity of Hint-1 is its ability to catalyze the conversion of adenosine 5'-O-monophosphorothioate (AMPS) to 5'-O-monophosphate (AMP). By mutagenetic and biochemical studies, we defined the active site of Hint-1 and the kinetic parameters of the desulfuration reaction (P-S bond cleavage). Additionally, crystallographic analysis (resolution from 1.08 to 1.37 Å) of three engineered cysteine mutants showed the high similarity of their structures, which were not very different from the structure of WT Hint-1. Moreover, we found that not only AMPS but also other ribonucleoside and 2'-deoxyribonucleoside phosphorothioates are desulfurated by Hint-1 at the following relative rates: GMPS > AMPS > dGMPS ≥ CMPS > UMPS > dAMPS ≫ dCMPS > TMPS, and during the reaction, hydrogen sulfide, which is thought to be the third gaseous mediator, was released.


    Organizational Affiliation

    Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz 90-363, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histidine triad nucleotide-binding protein 1
A
126Oryctolagus cuniculusMutation(s): 1 
Gene Names: HINT1 (HINT)
EC: 3.-.-.-
Find proteins for P80912 (Oryctolagus cuniculus)
Go to Gene View: HINT1
Go to UniProtKB:  P80912
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ADN
Query on ADN

Download SDF File 
Download CCD File 
A
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.132 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 39.965α = 90.00
b = 39.965β = 90.00
c = 141.700γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing
MAR345data collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description