3B4B

T. tengcongensis glmS ribozyme with G40A mutation, bound to glucosamine-6-phosphate and a substrate RNA with a 2'5'-phosphodiester linkage

• PDB DOI: https://doi.org/10.2210/pdb3B4B/pdb
• NAKB: 3B4B

• Classification: RNA
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis
• Mutation(s): No 


• Deposited: 2007-10-23 Released: 2007-12-11 
• Deposition Author(s): Klein, D.J., Ferre-D'Amare, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.200 (DCC) 

Literature

Essential Role of an Active-Site Guanine in glmS Ribozyme Catalysis.

Klein, D.J., Been, M.D., Ferre-D'Amare, A.R.

(2007) J Am Chem Soc 129: 14858-14859

• PubMed: 17990888 
• DOI: https://doi.org/10.1021/ja0768441
• Primary Citation of Related Structures:  
  3B4A, 3B4B, 3B4C


• PubMed Abstract: 
  

  The glmS ribozyme is a catalytic riboswitch that is activated for endonucleolytic cleavage by the coenzyme glucosamine-6-phosphate. Using kinetic assays and X-ray crystallography, we identify an active-site mutation of a conserved guanine that abolishes catalysis without perturbing coenzyme binding. Our results provide evidence that coenzyme function requires a specific nucleobase to interact with the nucleophile of the cleavage reaction.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.38 kDa 
• Atom Count: 3,096 
• Modelled Residue Count: 143 
• Deposited Residue Count: 151 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
glmS ribozyme substrate with 2'5'-phosphodiester linkage	A	26	Caldanaerobacter subterraneus subsp. tengcongensis

Entity ID: 2
Molecule	Chains	Length	Organism	Image
glmS ribozyme RNA	B	125	Caldanaerobacter subterraneus subsp. tengcongensis

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLP	C [auth A]	2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose C6 H14 N O8 P XHMJOUIAFHJHBW-UKFBFLRUSA-N
3AD	D [auth A]	3'-DEOXYADENOSINE C10 H13 N5 O3 OFEZSBMBBKLLBJ-BAJZRUMYSA-N
MG	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: 2.70 Å
• R-Value Free:  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.200 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.992	α = 90
b = 39.686	β = 90
c = 70.968	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-11 
Deposition Author(s): Klein, D.J., Ferre-D'Amare, A.R.

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Structure summary