1RZY

Crystal structure of rabbit Hint complexed with N-ethylsulfamoyladenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

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This is version 1.2 of the entry. See complete history


Literature

Biochemical, crystallographic, and mutagenic characterization of hint, the AMP-lysine hydrolase, with novel substrates and inhibitors

Krakowiak, A.K.Pace, H.C.Blackburn, G.M.Adams, M.Mekhalfia, A.Kaczmarek, R.Baraniak, J.Stec, W.J.Brenner, C.

(2004) J Biol Chem 279: 18711-18716

  • DOI: 10.1074/jbc.M314271200
  • Primary Citation of Related Structures:  
    1RZY

  • PubMed Abstract: 
  • Hint, histidine triad nucleotide-binding protein, is a universally conserved enzyme that hydrolyzes AMP linked to lysine and, in yeast, functions as a positive regulator of the RNA polymerase II C-terminal domain kinase, Kin28. To explore the biochemical and structural bases for the adenosine phosphoramidate hydrolase activity of rabbit Hint, we synthesized novel substrates linking a p-nitroaniline group to adenylate (AMP-pNA) and inhibitors that consist of an adenosine group and 5'-sulfamoyl (AdoOSO(2)NH(2)) or N-ethylsulfamoyl (AdoOSO(2)NHCH(2)CH(3)) group ...

    Hint, histidine triad nucleotide-binding protein, is a universally conserved enzyme that hydrolyzes AMP linked to lysine and, in yeast, functions as a positive regulator of the RNA polymerase II C-terminal domain kinase, Kin28. To explore the biochemical and structural bases for the adenosine phosphoramidate hydrolase activity of rabbit Hint, we synthesized novel substrates linking a p-nitroaniline group to adenylate (AMP-pNA) and inhibitors that consist of an adenosine group and 5'-sulfamoyl (AdoOSO(2)NH(2)) or N-ethylsulfamoyl (AdoOSO(2)NHCH(2)CH(3)) group. AMP-pNA is a suitable substrate for Hint that allowed characterization of the inhibitors; titration of each inhibitor into AMP-pNA assays revealed their K(i) values. The N-ethylsulfamoyl derivative has a 13-fold binding advantage over the sulfamoyl adenosine. The 1.8-A cocrystal structure of rabbit Hint with N-ethylsulfamoyl adenosine revealed a binding site for the ethyl group against Trp-123, a residue that reaches across the Hint dimer interface to interact with the alkyl portion of the inhibitor and, presumably, the alkyl portion of a lysyl substrate. Ser-107 is positioned to donate a hydrogen bond to the leaving group nitrogen. Consistent with a role in acid-base catalysis, the Hint S107A mutant protein displayed depressed catalytic activity.


    Related Citations: 
    • Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins
      Brenner, C., Garrison, P., Gilmour, J., Peisach, D., Ringe, D., Petsko, G.A., Lowenstein, J.M.
      (1997) Nat Struct Biol 4: 231

    Organizational Affiliation

    Structural Biology and Bioinformatics Program, Kimmel Cancer Center, Philadelphia, Pennsylvania 19107, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histidine triad nucleotide-binding protein 1A126Oryctolagus cuniculusMutation(s): 0 
Gene Names: HINT1HINT
EC: 3
UniProt
Find proteins for P80912 (Oryctolagus cuniculus)
Explore P80912 
Go to UniProtKB:  P80912
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80912
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5AS
Query on 5AS

Download Ideal Coordinates CCD File 
B [auth A]5'-O-(N-ETHYL-SULFAMOYL)ADENOSINE
C12 H18 N6 O6 S
ONCSLXAPOGUODU-WOUKDFQISA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5AS Binding MOAD:  1RZY Ki: 1250 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.888α = 90
b = 39.888β = 90
c = 142.286γ = 90
Software Package:
Software NamePurpose
crystaldata collection
d*TREKdata reduction
CNSrefinement
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance