3HIT

Crystal structure of Saporin-L1 in complex with the dinucleotide inhibitor, a transition state analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.

Ho, M.C.Sturm, M.B.Almo, S.C.Schramm, V.L.

(2009) Proc Natl Acad Sci U S A 106: 20276-20281

  • DOI: https://doi.org/10.1073/pnas.0911606106
  • Primary Citation of Related Structures:  
    3HIO, 3HIQ, 3HIS, 3HIT, 3HIV, 3HIW

  • PubMed Abstract: 

    Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple pi-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the pi-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common features of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H(2)O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar saporin
A, B
259Saponaria officinalisMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for Q2QEH4 (Saponaria officinalis)
Explore Q2QEH4 
Go to UniProtKB:  Q2QEH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2QEH4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DYN
Query on DYN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
5'-O-[(S)-{[(3R,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-({[(S)-hydroxy(3-hydroxypropoxy)phosphoryl]oxy}methyl)pyrrolidin-3-yl]oxy}(hydroxy)phosphoryl]-3'-O-[(R)-hydroxy(4-hydroxybutoxy)phosphoryl]-2'-O-methylguanosine
C30 H47 N10 O17 P3
QYBAOMLZOZKJGY-BLRDUOQJSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DYN Binding MOAD:  3HIT Ki: 6.4 (nM) from 1 assay(s)
PDBBind:  3HIT Ki: 6.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.716α = 78.65
b = 53.069β = 65.85
c = 54.491γ = 80.83
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references