Brand  (β version)

PDB ID: 4O5E

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Ligands
Code Name Style Show Link
1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine PoSSuM
MG Magnesium ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
Code Name Show
FMG 2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-7-methyl-6-oxo-6,9-dihydro-1h-purin-7-ium
Glycosylation
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Modification
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Structure summary

Code : 4O5E   PDBj   RCSB PDB   PDBe
Header : Transferase, Lyase/DNA
Title : Structure of human DNA polymerase complexed with N7MG in the template base paired with incoming non-hydrolyzable TTP
Release Data : 2014-07-02
Compound :
mol_id molecule chains
1 DNA polymerase beta A
ec: 2.7.7.7, 4.2.99.-
fragment: DNA polymerase beta
mol_id molecule chains
2 DNA (5'-D(*CP*CP*GP*AP*CP*(FMG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T
fragment: template DNA
other_details: template
mol_id molecule chains
3 DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3') P
fragment: up primer DNA
other_details: up primer
mol_id molecule chains
4 DNA (5'-D(P*GP*TP*CP*GP*G)-3') D
fragment: down primer DNA
other_details: down primer
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: POLB
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
other_details: synthetic template DNA
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
other_details: synthetic up primer
mol_id organism_scientific
4 Synthetic construct  (taxid:32630)
synthetic: yes
other_details: synthetic down primer
Authors : Koag, M.C., Lee, S.
Keywords : DNA binding, polymerase fold, nucleotidyl transfer, DNA, nucleus, Transferase, Lyase-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.5320 Å )
Citation :

Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine.

Koag, M.C.,Kou, Y.,Ouzon-Shubeita, H.  et al.
(2014)  Nucleic Acids Res.  42 : 8755 - 8766

PubMed: 24966350
DOI: 10.1093/nar/gku554

Reaction

Chain : A
UniProt : P06746 (DPOLB_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 -
-
a 5'-end 2'-deoxyribose-2'-deoxyribonucleotide-DNA = (2E,4S)- 4-hydroxypenten-2-al-5-phosphate + a 5'-end 5'-phospho-2'- deoxyribonucleoside-DNA + H(+) - PubMed:9572863, PubMed:9614142
-
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'-phospho-2'- deoxyribonucleoside-DNA + H(+) 4.2.99.18 PubMed:9614142
-
Cofactor: Evidence: Note:
Mg(2+) ECO:0000269 | PubMed:9287163
Binds 2 magnesium ions per subunit.