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(-) Description

Title :  A 3'-OH, 2',5'-PHOSPHODIESTER SUBSTITUTION IN THE HAIRPIN RIBOZYME ACTIVE SITE REVEALS SIMILARITIES WITH PROTEIN RIBONUCLEASES
 
Authors :  A. T. Torelli, R. C. Spitale, J. Krucinska, J. E. Wedekind
Date :  03 Apr 08  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  2', 5' Phosphodiester; Hairpin Ribozyme; Reaction- Intermediate; Transition-State Stabilization; Ribonuclease; Phosphoryl-Transfer, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. T. Torelli, R. C. Spitale, J. Krucinska, J. E. Wedekind
Shared Traits On The Reaction Coordinates Of Ribonuclease And An Rna Enzyme
Biochem. Biophys. Res. Commun. V. 371 154 2008
PubMed-ID: 18423397  |  Reference-DOI: 10.1016/J.BBRC.2008.04.036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 13-MER SUBSTRATE STRAND WITH 3'-OH, 2',5'- PHOSPHODIESTER COVALENTLY LINKING 5TH AND 6TH NUCLEOTIDES
    Chains: A
    Engineered: YES
    Other Details: THE SCISSILE PHOSPHATE WAS REPLACED WITH A 2',5'-PHOSPHODIESTER LINK
    Other Details - Source: STRAND SYNTHESIZED BY FIDELITY SYSTEMS, INC (GAITHERSBURG, MD) USING MODIFIED ADENOSINE PHOSPHORAMIDITE TO CREATE 3'-OH, 2',5'-PHOSPHODIESTER LINKAGE BETWEEN POSITIONS 5 AND 6. SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA.
    Synthetic: YES
 
Molecule 2 - 29-MER RIBOZYME STRAND WITH S9L SYNTHETIC LINKER AT 13TH POSITION
    Chains: B
    Engineered: YES
    Other Details: STRAND SYNTHESIZED BY DHARMACON (FAYETTE, CO) AND INCLUDES S9L LINKING RESIDUE IN PLACE OF NATURALLY- OCCURRING ADENOSINE 14. SEQUENCE OTHERWISE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA.
    Synthetic: YES
 
Molecule 3 - 19-MER RIBOZYME STRAND
    Chains: C
    Engineered: YES
    Other Details: STRAND SYNTHESIZED BY DHARMACON (FAYETTE, CO). SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NCO1Ligand/IonCOBALT HEXAMMINE(III)
2S9L1Mod. Nucleotide2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGENPHOSPHATE

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(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:RNA  Length:13
                                            
                  3cqs A  1 UCCCAGUCCACCG 13
                                    10   


Chain B from PDB  Type:DNA/RNA  Length:30
                                                             
                  3cqs B  2 CGGUGAGAAGGGxGGCAGAGAAACACACGA 31
                                    11  |     21        31
                                       14-S9L             


Chain C from PDB  Type:RNA  Length:19
                                                  
                  3cqs C 31 UCGUGGUACAUUACCUGCC 49
                                    40
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 Related Entries

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(-) Related Entries Specified in the PDB File

11ba THE STRUCTURE OF BOVINE SEMINAL RIBONUCLEASE ALSO CRYSTALLIZED WITH A 3'-OH, 2',5'-PHOSPHODIESTER SUBSTRATE ANALOG.
2p7e THE SAME MINIMAL HAIRPIN RIBOZYME SEQUENCE CRYSTALLIZED WITH VANADATE AS A TRANSITION-STATE MIMIC.
2p7f THE SAME MINIMAL HAIRPIN RIBOZYME SEQUENCE CRYSTALLIZED WITH A 3'-DEOXY, 2',5'-PHOSPHODIESTER SUBSTITUTION AT THE SITE OF CLEAVAGE.