Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 14.09 kDa 
• Atom Count: 961 
• Modelled Residue Count: 114 
• Deposited Residue Count: 126 
• Unique protein chains: 1

1RZY

Crystal structure of rabbit Hint complexed with N-ethylsulfamoyladenosine

• PDB DOI: 10.2210/pdb1RZY/pdb

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-29 Released: 2004-03-09 
• Deposition Author(s): Krakowiak, A.K., Pace, H.C., Blackburn, G.M., Adams, M., Mekhalfia, A., Kaczmarek, R., Baraniak, J., Stec, W.J., Brenner, C.

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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 

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

• PubMed: 14982931 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad nucleotide-binding protein 1	A	126	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: HINT1, HINT EC: 3
UniProt
Find proteins for P80912 (Oryctolagus cuniculus) Explore P80912  Go to UniProtKB:  P80912

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5AS	B [auth A]	5'-O-(N-ETHYL-SULFAMOYL)ADENOSINE C12 H18 N6 O6 S ONCSLXAPOGUODU-WOUKDFQISA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 39.888	α = 90
b = 39.888	β = 90
c = 142.286	γ = 90

Software Package:

Software Name	Purpose
crystal	data collection
d*TREK	data reduction
CNS	refinement
CrystalClear	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-29 
• Released Date: 2004-03-09 
Deposition Author(s): Krakowiak, A.K., Pace, H.C., Blackburn, G.M., Adams, M., Mekhalfia, A., Kaczmarek, R., Baraniak, J., Stec, W.J., Brenner, C.

Revision History  

• 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