Brand  (β version)

PDB ID: 3RMB

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Ligands
Code Name Style Show Link
Non-standard Residues
Code Name Show
CTG (5r,6s)-5,6-dihydro-5,6-dihydroxythymidine-5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
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Structure summary

Code : 3RMB   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol
Release Data : 2011-08-10
Compound :
mol_id molecule chains synonym
1 DNA polymerase A,B,C,D Gp43
ec: 2.7.7.7
mutation: D222A, D327A
mol_id molecule chains
2 DNA (5'-D(*CP*GP*CP*(CTG)P*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') E,G,I,K
other_details: DNA template
mol_id molecule chains
3 DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*A)-3') F,H,J,L
other_details: DNA primer
Source :
mol_id organism_scientific expression_system
1 Enterobacteria phage RB69  (taxid:12353) Escherichia coli  (taxid:469008)
gene: 43, gp43
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
mol_id organism_scientific
2
synthetic: yes
mol_id organism_scientific
3
synthetic: yes
Authors : Aller, P., Duclos, S., Wallace, S.S., Doublie, S.
Keywords : DNA LESION, THYMINE GLYCOL, PROTEIN-DNA COMPLEX, TRANSFERASE-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.6500 Å )
Citation :

A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex.

Aller, P.,Duclos, S.,Wallace, S.S.  et al.
(2011)  J.Mol.Biol.  412 : 22 - 34

PubMed: 21781974
DOI: 10.1016/j.jmb.2011.07.007

A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.

Aller, P.,Rould, M.A.,Hogg, M.  et al.
(2007)  Proc.Natl.Acad.Sci.USA  104 : 814 - 818

PubMed: 17210917
DOI: 10.1073/pnas.0606648104

Reaction

Chain : A, B, C, D
UniProt : Q38087 (DPOL_BPR69)
Reaction: EC: Evidence:
Physiological Direction:
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 2.7.7.7 HAMAP- Rule:MF_04100, PubMed:17098747, PubMed:18503083, PubMed:20795733, PubMed:22616982, PubMed:24116139
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