2P7F - JenaLib

Title :   THE NOVEL USE OF A 2',5'-PHOSPHODIESTER LINKAGE AS A REACTION INTERMEDIATE AT THE ACTIVE SITE OF A SMALL RIBOZYME

Authors :   A. T. Torelli, J. Krucinska, J. E. Wedekind

Date :   20 Mar 07 (Deposition) - 22 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Hairpin Ribozyme; 2', 5' Phosphodiester; Vanadate; Reaction Intermediate; Transition-State Stabilization; Active Site Waters; Induced Fit, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. T. Torelli, J. Krucinska, J. E. Wedekind
A Comparison Of Vanadate To A 2'-5' Linkage At The Active Site Of A Small Ribozyme Suggests A Role For Water In Transition-State Stabilization
Rna V. 13 1052 2007
PubMed-ID: 17488874 | Reference-DOI: 10.1261/RNA.510807
(for further references see the PDB file header)

Compounds

Molecule 1 - SUBSTRATE STRAND
	Chains	:	A
	Engineered	:	YES
	Other Details	:	2',5' PHOSPHODIESTER SUBSTITUTION AT THE SITE OF CLEAVAGE
	Other Details - Source	:	SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA
	Synthetic	:	YES

Molecule 2 - LOOP A RIBOZYME STRAND
	Chains	:	B
	Engineered	:	YES
	Other Details	:	SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA
	Synthetic	:	YES

Molecule 3 - LOOP B RIBOZYME STRAND
	Chains	:	C
	Engineered	:	YES
	Other Details	:	SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA
	Synthetic	:	YES

Molecule 4 - LOOP B S-TURN STRAND
	Chains	:	D
	Engineered	:	YES
	Other Details	:	CONTAINS THE S-TURN
	Other Details - Source	:	SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	U A:1 , C A:2 , NCO B:102	BINDING SITE FOR RESIDUE SO4 A 103
2	AC2	SOFTWARE	A C:20 , G C:21 , A D:40 , U D:41	BINDING SITE FOR RESIDUE NCO D 101
3	AC3	SOFTWARE	C A:2 , SO4 A:103 , G B:11 , G B:12 , G B:13	BINDING SITE FOR RESIDUE NCO B 102

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

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Chain A from PDB  Type:RNA  Length:13
                                            
                  2p7f A  1 UCCCaGUCCACCG 13
                                |   10   
                                |        
                                5-3DA

Chain B from PDB  Type:RNA  Length:12
                                           
                  2p7f B  2 CGGUGAGAAGGG 13
                                    11

Chain C from PDB  Type:RNA  Length:17
                                                
                  2p7f C 15 GGCAGAGAAACACACGA 31
                                    24

Chain D from PDB  Type:RNA  Length:19
                                                  
                  2p7f D 31 UCGUGGUACAUUACCUGCC 49
                                    40

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Classification and Annotation

SCOP Domains (0, 0)

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Pfam Domains (0, 0)

Gene Ontology (0, 0)

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