2P7D - JenaLib

Title :   A MINIMAL, 'HINGED' HAIRPIN RIBOZYME CONSTRUCT SOLVED WITH MIMICS OF THE PRODUCT STRANDS AT 2.25 ANGSTROMS RESOLUTION

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 :   2.25

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

Keywords :   Hairpin Ribozyme; Product Mimic; 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 - 5' SUBSTRATE STRAND, PENTAMERIC FRAGMENT
	Chains	:	A
	Engineered	:	YES
	Other Details	:	SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA
	Synthetic	:	YES

Molecule 2 - RIBOZYME STRAND I
	Chains	:	B
	Engineered	:	YES
	Other Details	:	DOMAIN-LINKING RESIDUE S9L AT THE 3'-END
	Other Details - Source	:	SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA
	Synthetic	:	YES

Molecule 3 - RIBOZYME STRAND II
	Chains	:	C
	Engineered	:	YES
	Other Details	:	DOMAIN-LINKING RESIDUE S9L AT THE 5'-END
	Other Details - Source	:	SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA
	Synthetic	:	YES

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

Molecule 5 - 3' SUBSTRATE STRAND, OCTAMERIC FRAGMENT
	Chains	:	P
	Engineered	:	YES
	Other Details	:	SEQUENCE OCCURS NATURALLY IN TOBACCO RINGSPOT VIRUS SATELLITE RNA
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (4, 4)

Asymmetric Unit (4, 4)

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 A:5 , G B:8	BINDING SITE FOR RESIDUE NA A 104
3	AC3	SOFTWARE	A C:20 , G C:21 , A D:40 , U D:41	BINDING SITE FOR RESIDUE NCO D 101
4	AC4	SOFTWARE	C A:2 , C A:3 , 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:5
                                    
                  2p7d A  1 UCCCA  5

Chain B from PDB  Type:DNA/RNA  Length:13
                                            
                  2p7d B  2 CGGUGAGAAGGGx 14
                                    11  |
                                       14-S9L

Chain C from PDB  Type:RNA  Length:17
                                                
                  2p7d C 15 GGCAGAGAAACACACGA 31
                                    24

Chain D from PDB  Type:RNA  Length:19
                                                  
                  2p7d D 31 UCGUGGUACAUUACCUGCC 49
                                    40

Chain P from PDB  Type:RNA  Length:8
                                       
                  2p7d P  6 GUCCACCG 13

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Classification and Annotation

SCOP Domains (0, 0)

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Gene Ontology (0, 0)

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