Biological Assembly 1  

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Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49564.59 
• Atom Count: 3097 
• Residue Count: 152 
• Unique nucleic acid chains: 2

2HO7

Pre-cleavage state of the Thermoanaerobacter tengcongensis glmS ribozyme bound to glucose-6-phosphate

• DOI: 10.2210/pdb2HO7/pdb
• NDB: UR0097

• Classification: RNA


• Deposited: 2006-07-13 Released: 2006-09-26 
• Deposition Author(s): Klein, D.J., Ferre-D'Amare, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.239 
• R-Value Work: 0.208 

Literature

Structural basis of glmS ribozyme activation by glucosamine-6-phosphate

Klein, D.J., Ferre-D'Amare, A.R.

(2006) Science 313: 1752-1756

• PubMed: 16990543 
• DOI: 10.1126/science.1129666
• Primary Citation of Related Structures:  
  2HO6, 2H0Z, 2H0X, 2H0W, 2H0S, 2GCV, 2GCS


• PubMed Abstract: 
  

The glmS ribozyme is the only natural catalytic RNA known to require a small-molecule activator for catalysis. This catalytic RNA functions as a riboswitch, with activator-dependent RNA cleavage regulating glmS messenger RNA expression. We report crystal structures of the glmS ribozyme in precleavage states that are unliganded or bound to the competitive inhibitor glucose-6-phosphate and in the postcleavage state. All structures superimpose closely, revealing a remarkably rigid RNA that contains a preformed active and coenzyme-binding site. Unlike other riboswitches, the glmS ribozyme binds its activator in an open, solvent-accessible pocket. Our structures suggest that the amine group of the glmS ribozyme-bound coenzyme performs general acid-base and electrostatic catalysis.

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Organizational Affiliation: 

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
glmS ribozyme substrate RNA	A	27	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
glmS ribozyme RNA	B	125	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
G6P	A	ALPHA-D-GLUCOSE-6-PHOSPHATE C6 H13 O9 P NBSCHQHZLSJFNQ-DVKNGEFBSA-N
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A23	B	RNA LINKING	C10 H13 N5 O9 P2		A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.239 
• R-Value Work: 0.208 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 181.443	α = 90.00
b = 40.840	β = 90.00
c = 72.097	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-13 
• Released Date: 2006-09-26 
• Deposition Author(s): Klein, D.J., Ferre-D'Amare, A.R.

Revision History 

• Version 1.0: 2006-09-26
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance