2HO7 | pdb_00002ho7

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

• PDB DOI: https://doi.org/10.2210/pdb2HO7/pdb
• NAKB: 2HO7

• Classification: RNA
• Mutation(s): No 


• 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: 2.90 Å
• R-Value Free: 
  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.200 (DCC) 

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: https://doi.org/10.1126/science.1129666
• Primary Citation of Related Structures:  
  2GCS, 2GCV, 2H0S, 2H0W, 2H0X, 2H0Z, 2HO6, 2HO7


• 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.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.56 kDa 
• Atom Count: 3,113 
• Modeled Residue Count: 144 
• Deposited Residue Count: 152 
• Unique nucleic acid chains: 2

Macromolecules

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G6P	C [auth A]	6-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-DVKNGEFBSA-N
MG	D [auth B], E [auth B], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.200 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.443	α = 90
b = 40.84	β = 90
c = 72.097	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Structure summary