3RTJ

Crystal structure of ricin bound with dinucleotide ApG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.198 

wwPDB Validation   3D Report Full Report



Literature

X-ray analysis of substrate analogs in the ricin A-chain active site.

Monzingo, A.F.Robertus, J.D.

(1992) J Mol Biol 227: 1136-1145

  • DOI: 10.1016/0022-2836(92)90526-p
  • Primary Citation of Related Structures:  
    3RTI, 3RTJ

  • PubMed Abstract: 
  • Ricin A-chain is an N-glycosidase that hydrolyzes the adenine ring from a specific adenosine of rRNA. Formycin monophosphate (FMP) and adenyl(3'-->5')guanosine (ApG) were bound to ricin A-chain and their structures elucidated by X-ray crystallography. Th ...

    Ricin A-chain is an N-glycosidase that hydrolyzes the adenine ring from a specific adenosine of rRNA. Formycin monophosphate (FMP) and adenyl(3'-->5')guanosine (ApG) were bound to ricin A-chain and their structures elucidated by X-ray crystallography. The formycin ring stacks between tyrosines 80 and 123 and at least four hydrogen bonds are made to the adenine moiety. A residue invariant in this enzyme class, Arg180, appears to hydrogen bond to N-3 of the susceptible adenine. Three hypothetical models for binding a true hexanucleotide substrate, CGAGAG, are proposed. They incorporate adenine binding, shown by crystallography, but also include geometry likely to favor catalysis. For example, efforts have been made to orient the ribose ring in a way that allows solvent attack and oxycarbonium stabilization by the enzyme. The favored model is a simple perturbation of the tetraloop structure determined by nuclear magnetic resonance for similar polynucleotides. The model is attractive in that specific roles are defined for conserved protein residues. A mechanism of action is proposed. It invokes oxycarbonium ion stabilization on ribose by Glu177 in the transition state. Arg180 stabilizes anion development on the leaving adenine by protonation at N-3 and may activate a trapped water molecule that is the ultimate nucleophile in the depurination.


    Organizational Affiliation

    Clayton Foundation Biochemical Institute, Department of Chemistry and Biochemistry, University of Texas, Austin 78712.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ricin A chain A267Ricinus communisMutation(s): 0 
EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis)
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Go to UniProtKB:  P02879
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ricin B chain B262Ricinus communisMutation(s): 0 
EC: 3.2.2.22
Find proteins for P02879 (Ricinus communis)
Explore P02879 
Go to UniProtKB:  P02879
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*G)-3')D2N/A
    Oligosaccharides

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    Entity ID: 4
    MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
    beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
    C, E
    2 N/A Oligosaccharides Interaction
    Entity ID: 5
    MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
    2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
    F, G
    2 N-Glycosylation Oligosaccharides Interaction
    Biologically Interesting Molecules (External Reference) 1 Unique
    Entity ID: 4
    IDChainsNameType/Class2D Diagram3D Interactions
    PRD_900004
    Query on PRD_900004
    C, Ebeta-lactoseOligosaccharide /  Nutrient

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    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.00 Å
    • R-Value Work: 0.198 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 72.74α = 90
    b = 78.49β = 90
    c = 114.34γ = 90
    Software Package:
    Software NamePurpose
    Sandata collection
    X-PLORmodel building
    X-PLORrefinement
    Sandata reduction
    Sandata scaling
    X-PLORphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2011-08-31
      Type: Initial release
    • Version 2.0: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Atomic model, Data collection, Derived calculations, Structure summary