2H0Z

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

PDB DOI: https://doi.org/10.2210/pdb2H0Z/pdb
NAKB: 2H0Z

Classification: RNA
Mutation(s): No

Deposited: 2006-05-15 Released: 2006-09-26
Deposition Author(s): Klein, D.J., Ferre-D'Amare, A.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.239 (Depositor), 0.230 (DCC)
R-Value Work:
0.206 (Depositor), 0.200 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 49.58 kDa
Atom Count: 3,112
Modelled Residue Count: 144
Deposited Residue Count: 152
Unique nucleic acid chains: 1
Unique hybrid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
glmS ribozyme deoxy RNA inhibitor	A	27	N/A
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
glmS ribozyme RNA	B	125	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G6P Query on G6P Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	6-O-phosphono-alpha-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-DVKNGEFBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A] E [auth B] F [auth B] G [auth B] H [auth B] D [auth A], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.239 (Depositor), 0.230 (DCC)
R-Value Work: 0.206 (Depositor), 0.200 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.877	α = 90
b = 39.809	β = 90
c = 70.226	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-09-26

Deposition Author(s):

Klein, D.J.

Ferre-D'Amare, A.R.

Revision History (Full details and data files)

Version 1.0: 2006-09-26
Type: Initial release
Version 1.1: 2008-04-01
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, Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Structure summary