3BO4

A relaxed active site following exon ligation by a group I intron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A relaxed active site after exon ligation by the group I intron

Lipchock, S.V.Strobel, S.A.

(2008) Proc.Natl.Acad.Sci.Usa 105: 5699-5704

  • DOI: 10.1073/pnas.0712016105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structur ...

    During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structures that examine the role of active-site metal ions during the second step of RNA splicing. These structures reveal a relaxed active site, in which direct metal coordination by the exons is lost after ligation, while other tertiary interactions are retained between the exon and the intron. Consistent with these structural observations, kinetic and thermodynamic measurements show that the scissile phosphate makes direct contact with metals in the ground state before exon ligation and in the transition state, but not after exon ligation. Despite no direct exonic interactions and even in the absence of the scissile phosphate, two metal ions remain bound within the active site. Together, these data suggest that release of the ligated exons from the intron is preceded by a change in substrate-metal coordination before tertiary hydrogen bonding contacts to the exons are broken.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein A
A
95Homo sapiensMutation(s): 2 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Go to Gene View: SNRPA
Go to UniProtKB:  P09012
Entity ID: 1
MoleculeChainsLengthOrganism
Group I intron P9B197synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*A)-D(P*DG)-3')C16synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(*CP*A)-D(P*DU)-R(P*AP*CP*GP*GP*CP*C)-3')D9synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
A23
Query on A23
B
RNA LINKINGC10 H13 N5 O9 P2A
GTP
Query on GTP
B
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.280 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 111.188α = 90.00
b = 111.188β = 90.00
c = 240.300γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description, Source and taxonomy