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(-) Description

Title :  METHYLATION OF CYTOSINE AT C5 IN A CPG SEQUENCE CONTEXT CAUSES A CONFORMATIONAL SWITCH OF A BENZO[A]PYRENE DIOL EPOXIDE-N2-GUANINE ADDUCT IN DNA FROM A MINOR GROOVE ALIGNMENT TO INTERCALATION WITH BASE DISPLACEMENT
 
Authors :  N. Zhang, C. Lin, X. Huang, A. Kolbanovskiy, B. E. Hingerty, S. Amin, S. Broyde, N. E. Geacintov, D. J. Patel
Date :  15 Dec 04  (Deposition) - 22 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (9x)
Keywords :  Conformational Switch, Cytosine Methylation, P53 Mutation Hot Spot, Dna Adduct, Benzo[A]Pyrene, Bpde (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Zhang, C. Lin, X. Huang, A. Kolbanovskiy, B. E. Hingerty, S. Amin, S. Broyde, N. E. Geacintov, D. J. Patel
Methylation Of Cytosine At C5 In A Cpg Sequence Context Causes A Conformational Switch Of A Benzo[A]Pyrene Diol Epoxide-N2-Guanine Adduct In Dna From A Minor Groove Alignment To Intercalation With Base Displacement.
J. Mol. Biol. V. 346 951 2005
PubMed-ID: 15701509  |  Reference-DOI: 10.1016/J.JMB.2004.12.027
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*CP*AP*TP*(5CM)P*(BPG)P*CP*TP*AP*CP*C)- 3'
    Chains: A
    Engineered: YES
    Other Details: BP ATTACHED TO G6, METHYLATION OF C5
    Synthetic: YES
 
Molecule 2 - 5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (9x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2BAP1Ligand/Ion1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARE5CM A:5 , DG A:6 , DC A:7 , DT A:8 , DG B:16 , DG B:18BINDING SITE FOR RESIDUE BAP A 23

(-) SS Bonds  (0, 0)

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(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:DNA  Length:11
                                          
                  1y9h A  1 CCATcGCTACC 11
                                |   10 
                                |      
                                5-5CM  


Chain B from PDB  Type:DNA  Length:11
                                          
                  1y9h B 12 GGTAGCGATGG 22
                                    21
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
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