2NZ4

Structural investigation of the GlmS ribozyme bound to its catalytic cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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This is version 1.5 of the entry. See complete history


Literature

Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor

Cochrane, J.C.Lipchock, S.V.Strobel, S.A.

(2007) Chem Biol 14: 97-105

  • DOI: https://doi.org/10.1016/j.chembiol.2006.12.005
  • Primary Citation of Related Structures:  
    2NZ4

  • PubMed Abstract: 

    The GlmS riboswitch is located in the 5'-untranslated region of the gene encoding glucosamine-6-phosphate (GlcN6P) synthetase. The GlmS riboswitch is a ribozyme with activity triggered by binding of the metabolite GlcN6P. Presented here is the structure of the GlmS ribozyme (2.5 A resolution) with GlcN6P bound in the active site. The GlmS ribozyme adopts a compact double pseudoknot tertiary structure, with two closely packed helical stacks. Recognition of GlcN6P is achieved through coordination of the phosphate moiety by two hydrated magnesium ions as well as specific nucleobase contacts to the GlcN6P sugar ring. Comparison of this activator bound and the previously published apoenzyme complex supports a model in which GlcN6P does not induce a conformational change in the RNA, as is typical of other riboswitches, but instead functions as a catalytic cofactor for the reaction. This demonstrates that RNA, like protein enzymes, can employ the chemical diversity of small molecules to promote catalytic activity.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
U1 Small Nuclear Ribonucleoprotein AI [auth A],
J [auth B],
K [auth C],
L [auth D]
94Homo sapiensMutation(s): 2 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
GTEx:  ENSG00000077312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
substrate strand RNA 13-merA [auth E],
C [auth F],
E [auth G],
G [auth H]
13N/A
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
GlmS ribozymeB [auth P],
D [auth Q],
F [auth R],
H [auth S]
141N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLP
Query on GLP

Download Ideal Coordinates CCD File 
BA [auth H],
M [auth P],
R [auth F],
W [auth G]
2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose
C6 H14 N O8 P
XHMJOUIAFHJHBW-UKFBFLRUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth R]
CA [auth H]
DA [auth H]
EA [auth S]
FA [auth S]
AA [auth R],
CA [auth H],
DA [auth H],
EA [auth S],
FA [auth S],
N [auth P],
O [auth P],
P,
Q [auth P],
S [auth F],
T [auth Q],
U [auth Q],
V [auth Q],
X [auth G],
Y [auth R],
Z [auth R]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.127α = 90
b = 234.157β = 90.65
c = 105.003γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2021-10-20
    Changes: Database references, Structure summary
  • Version 1.5: 2023-12-27
    Changes: Data collection, Refinement description