429D

CRYSTAL STRUCTURE OF A LEADZYME; METAL BINDING AND IMPLICATIONS FOR CATALYSIS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis.

Wedekind, J.E., McKay, D.B.

(1999) Nat.Struct.Mol.Biol. 6: 261-268

  • DOI: 10.1038/6700

  • PubMed Abstract: 

    • The leadzyme is a small RNA motif that catalyzes a site-specific, Pb2+-dependent cleavage reaction. As such, it is an example of a metal-dependent RNA enzyme. Here we describe the X-ray crystallographic structure of the leadzyme, which reveals two in ...

    The leadzyme is a small RNA motif that catalyzes a site-specific, Pb2+-dependent cleavage reaction. As such, it is an example of a metal-dependent RNA enzyme. Here we describe the X-ray crystallographic structure of the leadzyme, which reveals two independent molecules per asymmetric unit. Both molecules feature an internal loop in which a bulged purine base stack twists away from the helical stem. This kinks the backbone, rendering the phosphodiester bond susceptible to cleavage. The independent molecules have different conformations: one leadzyme copy coordinates Mg2+, whereas the other binds only Ba2+ or Pb2+. In the active site of the latter molecule, a single Ba2+ ion coordinates the 2'-OH nucleophile, and appears to mimic the binding of catalytic lead. These observations allow a bond cleavage reaction to be modeled, which reveals the minimal structural features necessary for catalysis by this small ribozyme.

    Organizational Affiliation: 

    Department of Structural Biology, Stanford University School of Medicine, California 94305-5126, USA. Wedekind@ribose.stanford.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3')A,C13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3')B,D11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.255 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 60.400α = 90.00
b = 60.400β = 90.00
c = 133.100γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
DENZOdata reduction
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-01
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance