6B42

Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) 2'-deoxy-AMP complex at 1.13A resolution

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2017-09-25 Released: 2017-10-18 
  • Deposition Author(s): Maize, K.M., Finzel, B.C.
  • Funding Organization(s): Minnesota Dept. of Employment and Economic Development; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Crystal Structure Based Guide to the Design of Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) Activated ProTides.

Maize, K.M.Shah, R.Strom, A.Kumarapperuma, S.Zhou, A.Wagner, C.R.Finzel, B.C.

(2017) Mol. Pharm. 14: 3987-3997

  • DOI: 10.1021/acs.molpharmaceut.7b00664
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nucleotide analogues that incorporate a metabolically labile nucleoside phosphoramidate (a ProTide) have found utility as prodrugs. In humans, ProTides can be cleaved by human histidine triad nucleotide binding protein 1 (hHint1) to expose the nucleo ...

    Nucleotide analogues that incorporate a metabolically labile nucleoside phosphoramidate (a ProTide) have found utility as prodrugs. In humans, ProTides can be cleaved by human histidine triad nucleotide binding protein 1 (hHint1) to expose the nucleotide monophosphate. Activation by this route circumvents highly selective nucleoside kinases that limit the use of nucleosides as prodrugs. To better understand the diversity of potential substrates of hHint1, we created and studied a series of phosphoramidate nucleosides. Using a combination of enzyme kinetics, X-ray crystallography, and isothermal titration calorimetry with both wild-type and inactive mutant enzymes, we have been able to explore the energetics of substrate binding and establish a structural basis for catalytic efficiency. Diverse nucleobases are well tolerated, but portions of the ribose are needed to position substrates for catalysis. Beneficial characteristics of the amine leaving group are also revealed. Structural principles revealed by these results may be exploited to tune the rate of substrate hydrolysis to strategically alter the intracellular release of the product nucleoside monophosphate from the ProTide.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histidine triad nucleotide-binding protein 1
A
129Homo sapiensMutation(s): 0 
Gene Names: HINT1 (HINT, PKCI1, PRKCNH1)
EC: 3.-.-.-
Find proteins for P49773 (Homo sapiens)
Go to Gene View: HINT1
Go to UniProtKB:  P49773
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D5M
Query on D5M

Download SDF File 
Download CCD File 
A
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.154 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 39.738α = 90.00
b = 39.738β = 90.00
c = 141.133γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Minnesota Dept. of Employment and Economic DevelopmentUnited StatesSPAP-06-0014-P-FY07
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM08700

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references
  • Version 1.2: 2017-12-06
    Type: Author supporting evidence