4EQH

Crystal structure of histidine triad nucleotide-binding protein 1 (HINT1) from human complexed with Trp-AMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.668 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Side chain independent recognition of aminoacyl adenylates by the hint1 transcription suppressor.

Wang, J.Fang, P.Schimmel, P.Guo, M.

(2012) J.Phys.Chem.B 116: 6798-6805

  • DOI: 10.1021/jp212457w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human Hint1 suppresses specific gene transcription by interacting with the transcription factor MITF in mast cells. Hint1 activity is connected to lysyl-tRNA synthetase (LysRS), a member of the universal aminoacyl tRNA synthetase family that catalyze ...

    Human Hint1 suppresses specific gene transcription by interacting with the transcription factor MITF in mast cells. Hint1 activity is connected to lysyl-tRNA synthetase (LysRS), a member of the universal aminoacyl tRNA synthetase family that catalyzes specific aminoacylation of their cognate tRNAs, through an aminoacyl adenylate (aa-AMP) intermediate. During immune activation, LysRS produces a side-product diadenosine tetraphosphate (Ap(4)A) from the condensation of Lys-AMP with ATP. The pleiotropic signaling molecule Ap(4)A then binds Hint1 to promote activation of MITF-target gene transcription. Earlier work showed that Hint1 can also bind and hydrolyze Lys-AMP, possibly to constrain Ap(4)A production. Because Ap(4)A can result from condensation of other aa-AMP's with ATP, the specificity of the Hint1 aa-AMP-hydrolysis activity is of interest. Here we show that Hint1 has broad specificity for adenylate hydrolysis, whose structural basis we revealed through high-resolution structures of Hint1 in complex with three different aa-AMP analogues. Hint1 recognizes only the common main chain of the aminoacyl moiety, and has no contact with the aa side chain. The α-amino group is anchored by a cation-pi interaction with Trp123 at the C-terminus of Hint1. These results reveal the structural basis for the remarkable adenylate surveillance activity of Hint1, to potentially control Ap(4)A levels in the cell.


    Organizational Affiliation

    Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histidine triad nucleotide-binding protein 1
A, B
128Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
WSA
Query on WSA

Download SDF File 
Download CCD File 
B
5'-O-[(L-TRYPTOPHYLAMINO)SULFONYL]ADENOSINE
C21 H24 N8 O7 S
RQAVKMXDGHWLGD-BFNSABJLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.668 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.000α = 90.00
b = 46.427β = 95.24
c = 63.884γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
DENZOdata reduction
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-06-27
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description