3G8S

Crystal structure of the pre-cleaved Bacillus anthracis glmS ribozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme

Cochrane, J.C.Lipchock, S.V.Smith, K.D.Strobel, S.A.

(2009) Biochemistry 48: 3239-3246

  • DOI: 10.1021/bi802069p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The glmS ribozyme is the first naturally occurring catalytic RNA that relies on an exogenous, nonnucleotide cofactor for reactivity. From a biochemical perspective, the glmS ribozyme derived from Bacillus anthracis is the best characterized. However, ...

    The glmS ribozyme is the first naturally occurring catalytic RNA that relies on an exogenous, nonnucleotide cofactor for reactivity. From a biochemical perspective, the glmS ribozyme derived from Bacillus anthracis is the best characterized. However, much of the structural work to date has been done on a variant glmS ribozyme, derived from Thermoanaerobacter tengcongensis. Here we present structures of the B. anthracis glmS ribozyme in states before the activating sugar, glucosamine 6-phosphate (GlcN6P), has bound and after the reaction has occurred. These structures show an active site preorganized to bind GlcN6P that retains some affinity for the sugar even after cleavage of the RNA backbone. A structure of an inactive glmS ribozyme with a mutation distal from the ligand-binding pocket highlights a nucleotide critical to the reaction that does not affect GlcN6P binding. Structures of the glmS ribozyme bound to a naturally occurring inhibitor, glucose 6-phosphate (Glc6P), and a nonnatural activating sugar, mannosamine 6-phosphate (MaN6P), reveal a binding mode similar to that of GlcN6P. Kinetic analyses show a pH dependence of ligand binding that is consistent with titration of the cofactor's phosphate group and support a model in which the major determinant of activity is the sugar amine independent of its stereochemical presentation.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
A, B, C, D
98Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')E,F,G,H13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
GLMS RIBOZYMEP,Q,R,S141N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
E, H, P, Q, R, S
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
E, F, G, H
RNA LINKINGC11 H16 N5 O7 PA
GTP
Query on GTP
P, Q, R, S
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.364α = 90.00
b = 228.480β = 90.58
c = 103.915γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data collection
MOLREPphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description