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(-) Description

Title :  CLASS II LIGASE RIBOZYME PRODUCT-TEMPLATE DUPLEX, STRUCTURE 1
 
Authors :  J. N. Pitt, A. R. Ferre-D'Amare
Date :  13 Jan 09  (Deposition) - 24 Feb 09  (Release) - 31 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ribozyme, Ligase, 2'-5', 2-5, 2P5, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Pitt, A. R. Ferre-D'Amare
Structure-Guided Engineering Of The Regioselectivity Of Rna Ligase Ribozymes.
J. Am. Chem. Soc. V. 131 3532 2009
PubMed-ID: 19220054  |  Reference-DOI: 10.1021/JA8067325
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*GP*UP*GP*UP*GP*AP*GP*GP*CP*UP*G)-3'
    Chains: A, C
    Engineered: YES
    Other Details: TEMPLATE STAND OF THE CLASS II LIGASE A4-11
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*CP*AP*GP*UP*CP*GP*GP*AP*AP*CP*A)-3'
    Chains: B, D
    Engineered: YES
    Other Details: PRODUCT STRAND OF THE CLASS II LIGASE A4-11, SINGLE STRANDED RNA WITH ONE 2'-5' LINKAGE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
2MG9Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREA B:3 , HOH B:315BINDING SITE FOR RESIDUE MG B 201
02AC2SOFTWAREA D:3BINDING SITE FOR RESIDUE K D 202
03AC3SOFTWAREA B:3 , A B:4BINDING SITE FOR RESIDUE MG B 203
04AC4SOFTWAREG A:43 , G A:53 , HOH A:309 , HOH A:310BINDING SITE FOR RESIDUE MG A 204
05AC5SOFTWAREG C:53BINDING SITE FOR RESIDUE MG C 205
06AC6SOFTWAREA A:48 , A D:4 , C D:5BINDING SITE FOR RESIDUE MG A 306
07AC7SOFTWAREC A:51 , U B:-2BINDING SITE FOR RESIDUE MG B 308
08AC8SOFTWAREG A:47 , A A:48 , G B:1BINDING SITE FOR RESIDUE MG B 312
09AC9SOFTWAREU C:46BINDING SITE FOR RESIDUE MG C 316
10BC1SOFTWAREG A:53 , C D:-1 , U D:-2BINDING SITE FOR RESIDUE K D 319
11BC2SOFTWAREU C:46 , G C:47 , G D:1 , G D:2BINDING SITE FOR RESIDUE MG C 322

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric Unit
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Chain A from PDB  Type:RNA  Length:11
                                          
                  3ftm A 43 GUGUGAGGCUG 53
                                    52 


Chain B from PDB  Type:RNA  Length:12
                                           
                  3ftm B -6 CCAGUCGGAACA  6
                                 ||  4  
                                -1|     
                                  1     


Chain C from PDB  Type:RNA  Length:11
                                          
                  3ftm C 43 GUGUGAGGCUG 53
                                    52 


Chain D from PDB  Type:RNA  Length:12
                                           
                  3ftm D -6 CCAGUCGGAACA  6
                                 ||  4  
                                -1|     
                                  1
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(-) Gene Ontology  (0, 0)

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3fs0 HIGHER RESOLUTION CRYSTAL FORM OF SIMILAR CLASS II PRODUCT- TEMPLATE DUPLEX