2Z75

T. tengcongensis glmS ribozyme bound to glucosamine-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.226 

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This is version 1.3 of the entry. See complete history


Literature

Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme

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

(2007) J Mol Biol 373: 178-189

  • DOI: 10.1016/j.jmb.2007.07.062
  • Primary Citation of Related Structures:  
    2Z74, 2Z75

  • PubMed Abstract: 
  • The glmS ribozyme is a catalytic RNA that self-cleaves at its 5'-end in the presence of glucosamine 6-phosphate (GlcN6P). We present structures of the glmS ribozyme from Thermoanaerobacter tengcongensis that are bound with the cofactor GlcN6P or the inhibitor glucose 6-phosphate (Glc6P) at 1 ...

    The glmS ribozyme is a catalytic RNA that self-cleaves at its 5'-end in the presence of glucosamine 6-phosphate (GlcN6P). We present structures of the glmS ribozyme from Thermoanaerobacter tengcongensis that are bound with the cofactor GlcN6P or the inhibitor glucose 6-phosphate (Glc6P) at 1.7 A and 2.2 A resolution, respectively. The two structures are indistinguishable in the conformations of the small molecules and of the RNA. GlcN6P binding becomes apparent crystallographically when the pH is raised to 8.5, where the ribozyme conformation is identical with that observed previously at pH 5.5. A key structural feature of this ribozyme is a short duplex (P2.2) that is formed between sequences just 3' of the cleavage site and within the core domain, and which introduces a pseudoknot into the active site. Mutagenesis indicates that P2.2 is required for activity in cis-acting and trans-acting forms of the ribozyme. P2.2 formation in a trans-acting ribozyme was exploited to demonstrate that N1 of the guanine at position 1 contributes to GlcN6P binding by interacting with the phosphate of the cofactor. At neutral pH, RNAs with adenine, 2-aminopurine, dimethyladenine or purine substitutions at position 1 cleave faster with glucosamine than with GlcN6P. This altered cofactor preference provides biochemical support for the orientation of the cofactor within the active site. Our results establish two features of the glmS ribozyme that are important for its activity: a sequence within the core domain that selects and positions the cleavage-site sequence, and a nucleobase at position 1 that helps position GlcN6P.


    Organizational Affiliation

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



Macromolecules
Find similar nucleic acids by: Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
glmS ribozyme substrate RNAA27Caldanaerobacter subterraneus subsp. tengcongensis MB4
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
glmS ribozyme RNAB125Caldanaerobacter subterraneus subsp. tengcongensis MB4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLP (Subject of Investigation/LOI)
Query on GLP

Download Ideal Coordinates CCD File 
C [auth A]2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose
C6 H14 N O8 P
XHMJOUIAFHJHBW-UKFBFLRUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth B] , E [auth B] , F [auth B] , G [auth B] , H [auth B] , I [auth B] , J [auth B] , K [auth B] , 
D [auth B],  E [auth B],  F [auth B],  G [auth B],  H [auth B],  I [auth B],  J [auth B],  K [auth B],  L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.935α = 90
b = 39.942β = 90
c = 70.435γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary