Extended Data Figure 4: Active sites of RNA-ligating nucleic acid enzymes.
From Crystal structure of a DNA catalyst
- Almudena Ponce-Salvatierra1, 2,
- Katarzyna Wawrzyniak-Turek1, 3,
- Ulrich Steuerwald2,
- Claudia Höbartner1, 3,
- Vladimir Pena2,
- Journal name:
- Nature
- Volume:
- 529,
- Pages:
- 231–234
- Date published:
- DOI:
- doi:10.1038/nature16471
Left: deoxyribozyme 9DB1; middle: class I ribozyme; right: L1 ligase ribozyme. Figure was generated using Protein Data Bank (PDB) accession numbers 5CKK (9DB1), 3R1L (class I) and 2OIU (L1).
Additional data
Affiliations
-
Max Planck Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Almudena Ponce-Salvatierra,
- Katarzyna Wawrzyniak-Turek &
- Claudia Höbartner
-
Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Almudena Ponce-Salvatierra,
- Ulrich Steuerwald &
- Vladimir Pena
-
Institute for Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
- Katarzyna Wawrzyniak-Turek &
- Claudia Höbartner
Contributions
Crystallographic work was performed by A.P.-S. under the supervision of V.P., biochemical experiments were performed by A.P.-S., K.W.-T. and C.H. U.S. obtained initial crystals. A.P.-S., V.P. and C.H. designed the experiments and all authors discussed the results and contributed to the manuscript.
Competing financial interests
The authors declare no competing financial interests.
Structural models and structure factors have been deposited in the Protein Data Bank under accession numbers 5CKI (cobalt) and 5CKK (native).
Author details
Almudena Ponce-Salvatierra
Search for this author in:
Katarzyna Wawrzyniak-Turek
Search for this author in:
Ulrich Steuerwald
Search for this author in:
Claudia Höbartner
Search for this author in:
Vladimir Pena
Search for this author in:
-
Extended Data Figure 1: Semi-continuous helix in the crystal lattice.
Hover over figure to zoomNucleotides important for the crystal contacts are labelled accordingly.
-
Extended Data Figure 2: Influence of 2′-modifications on mutant acceptor RNA U-1.
Hover over figure to zoom -
Extended Data Figure 3: Distribution of pseudorotation phase angels of 9DB1 deoxyribozyme in comparison with twister46 and L1 ligase ribozyme30.
Hover over figure to zoom -
Extended Data Figure 4: Active sites of RNA-ligating nucleic acid enzymes.
Hover over figure to zoomLeft: deoxyribozyme 9DB1; middle: class I ribozyme; right: L1 ligase ribozyme. Figure was generated using Protein Data Bank (PDB) accession numbers 5CKK (9DB1), 3R1L (class I) and 2OIU (L1).
-
Extended Data Figure 5: Positioning of the reactive nucleotides in the active centre of ligase deoxyribozyme 9DB1 in comparison to ribozymes.
Hover over figure to zoomA schematic of the three enzymes is shown before and after the crystal structure determination (left and central columns, respectively). Strands that were deliberately chosen are depicted in red and blue, while the ones that resulted from random selection are shown in black. Nucleotides at the ligation junction are coloured in cyan, stacking nucleotides are depicted in light red. Nucleotides shown as white-filled circles are indicated for orientation purposes. Recognition between reactive and pairing nucleotides is shown as dashed lines (left column). Structures of product-bound nucleic acid enzymes are compared (PDB accessions 5CKK (9DB1), 3HHN (class I) and 2OIU (L1), right column).
-
Extended Data Table 1: Data collection and refinement statistics
Hover over figure to zoomOne crystal was used for each data set. Highest-resolution shell values are shown in parentheses.
-
Extended Data Table 2: Oligonucleotides for kinetic experiments
Hover over figure to zoom*Catalytic core is underlined.
†dT29 is in bold.
‡Ligation site is indicated with |.
