Macromolecule Content

• Total Structure Weight: 9761.91 
• Atom Count: 647 
• Residue Count: 30 
• Unique nucleic acid chains: 1

2LDZ

SOLUTION STRUCTURE OF THE LEAD-DEPENDENT RIBOZYME, NMR, MINIMIZED AVERAGE STRUCTURE

• DOI: 10.2210/pdb2LDZ/pdb
• NDB: 2LDZ

• Classification: RNA


• Deposited: 1998-08-18 Released: 1999-02-23 
• Deposition Author(s): Hoogstraten, C.G., Legault, P., Pardi, A.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 25 
• Conformers Submitted: 1 
• Selection Criteria: NO NOE VIOLATIONS GREATER THAN 0.3 A, NO DIHEDRAL VIOLATIONS GREATER THAN 3 DEGREES, GOOD STEREOCHEMICAL QUALITY, TOTAL ENERGY LESS THAN -120 KCAL/MOL, NOE PSEUDOENERGY LESS THAN 4 KCAL/ MOL 

Literature

NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis.

Hoogstraten, C.G., Legault, P., Pardi, A.

(1998) J.Mol.Biol. 284: 337-350

• PubMed: 9813122 
• DOI: 10.1006/jmbi.1998.2182
• Primary Citation of Related Structures:  
  1LDZ


• PubMed Abstract: 
  

The NMR solution structure of a lead-dependent ribozyme, known as the leadzyme, is presented. This ribozyme is among the smallest of the known catalytic RNAs, with an active site consisting of a six-nucleotide asymmetric internal loop. This loop has a roughly double-helical structure, including a protonated adenine-cytosine wobble base-pair, that positions the cytosine base 5' to the cleavage site in a double-helical conformation. The deviations from helical structure consist of two bulged guanosine residues, G7 and G9, where G7 is the residue 3' to the cleavage site. The scissile phosphate group of the leadzyme is not positioned for in-line nucleophilic attack. Therefore, a conformational rearrangement in the active site is required to reach the proposed transition state for this ribozyme. This is similar to previous observations in X-ray studies of the hammerhead ribozyme, and emphasizes the necessity for dynamic structural fluctuations in the catalytic mechanism of small ribozymes. A model for metal-binding in the leadzyme is proposed in which a lead ion binds to a bulged guanine base that is critical for leadzyme function.

---

Related Citations: 

• A Small Metalloribozyme with a Two-Step Mechanism
  Pan, T.,Uhlenbeck, O.C.
  (1992) Nature 358: 560
• Properties of an in Vitro Selected Pb2+ Cleavage Motif
  Pan, T.,Dichtl, B.,Uhlenbeck, O.C.
  (1994) Biochemistry 33: 9561
• In Vitro Selection of Rnas that Undergo Autolytic Cleavage with Pb2+
  Pan, T.,Uhlenbeck, O.C.
  (1992) Biochemistry 31: 3887
• Order, Dynamics and Metal-Binding in the Lead-Dependent Ribozyme
  Legault, P.,Hoogstraten, C.G.,Metlitzky, E.,Pardi, A.
  (1998) J.Mol.Biol. 284: 325




---

Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Colorado Boulder, Campus Box 215, Boulder, CO, 80309, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
LEAD-DEPENDENT RIBOZYME	A	30	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 25 
• Conformers Submitted: 1 
• Selection Criteria: NO NOE VIOLATIONS GREATER THAN 0.3 A, NO DIHEDRAL VIOLATIONS GREATER THAN 3 DEGREES, GOOD STEREOCHEMICAL QUALITY, TOTAL ENERGY LESS THAN -120 KCAL/MOL, NOE PSEUDOENERGY LESS THAN 4 KCAL/ MOL 

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-08-18 
• Released Date: 1999-02-23 
• Deposition Author(s): Hoogstraten, C.G., Legault, P., Pardi, A.

Revision History 

• Version 1.0: 1999-02-23
  Type: Initial release
• Version 1.1: 2008-03-05
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance