Brand  (β version)

PDB ID: 3VK8

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

Structure summary

Code : 3VK8   PDBj   RCSB PDB   PDBe
Header : HYDROLASE/DNA
Title : Crystal structure of DNA-glycosylase bound to DNA containing Thymine glycol
Release Data : 2011-12-14
Compound :
mol_id molecule chains synonym
1 Probable formamidopyrimidine-DNA glycosylase A,B Fapy-DNA glycosylase, DNA-(apurinic or apyrimidinic site) lyase, AP lyase
ec: 3.2.2.23, 4.2.99.18
mutation: E3Q
mol_id molecule chains
2 DNA (5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3') C,E
other_details: complementary DNA
mol_id molecule chains
3 DNA (5'-D(*CP*GP*TP*CP*CP*AP*(CTG)P*GP*TP*CP*TP*AP*C)-3') D,F
other_details: DNA containing Thymine glycol
Source :
mol_id organism_scientific organism_common expression_system
1 Acanthamoeba polyphaga mimivirus  (taxid:212035) APMV Escherichia coli  (taxid:562)
gene: MIMI_L315
expression_system_strain: Rosetta(DE3)pLys
expression_system_vector_type: plasmid
expression_system_plasmid: pET22b
mol_id organism_scientific
2
synthetic: yes
mol_id organism_scientific
3
synthetic: yes
Authors : Imamura, K., Averill, A., Wallace, S.S., Doublie, S.
Keywords : DNA glycosylase, hNEIL1 ortholog, DNA LESION, Thymine glycol, Zincless finger, DNA binding, HYDROLASE-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.0000 Å )
Citation :

Structural characterization of viral ortholog of human DNA glycosylase NEIL1 bound to thymine glycol or 5-hydroxyuracil-containing DNA

Imamura, K.,Averill, A.,Wallace, S.S.  et al.
(2012)  J.Biol.Chem.  287 : 4288 - 4298

PubMed: 22170059
DOI: 10.1074/jbc.M111.315309

Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA

Imamura, K.,Wallace, S.S.,Doublie, S.
(2009)  J.Biol.Chem.  284 : 26174 - 26183

PubMed: 19625256
DOI: 10.1074/jbc.M109.021907

Reaction

Chain : A, B
UniProt : Q5UQ00 (FPG_MIMIV)
Reaction: EC: Evidence:
Physiological Direction:
Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N- methyl)formamidopyrimidine. 3.2.2.23 -
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2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'- deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho- 2'-deoxyribonucleoside-DNA + H(+) 4.2.99.18 PROSITE- ProRule:PRU00392
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