Brand  (β version)

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Ligands
Code Name Style Show Link
EDO 1,2-ethanediol
F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
MN Manganese (II) ion
NA Sodium ion
Non-standard Residues
Code Name Show
3DR 1',2'-dideoxyribofuranose-5'-phosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show
Code : 3ISD   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : Ternary complex of human DNA polymerase beta with an abasic site (THF): DAPCPP mismatch
Release Data : 2009-09-15
Compound :
mol_id molecule chains
1 DNA polymerase beta A
ec: 2.7.7.7,4.2.99.-
mol_id molecule chains
2 5'-D(P*GP*TP*CP*GP*G)-3' D
mol_id molecule chains
3 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3' P
mol_id molecule chains
4 5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' T
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: POLB
expression_system_strain: TAP56
expression_system_vector_type: Plasmid
expression_system_plasmid: pWL11
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
other_details: chemically sytnthesized oligonucleotide
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
other_details: chemically sytnthesized oligonucleotide
mol_id organism_scientific
4 Synthetic construct  (taxid:32630)
synthetic: yes
other_details: chemically sytnthesized oligonucleotide
Authors : Beard, W.A., Shock, D.D., Batra, V.K., Pedersen, L.C., Wilson, S.H.
Keywords : Nucleotidyl Transferase, DNA Polymerase Beta, abasic site, Tetrahydrofuran, Ternary complex, gapped DNA, 'A-rule', DNA damage, DNA repair, DNA replication, DNA synthesis, DNA-binding, DNA-directed DNA polymerase, Lyase, Magnesium, Metal-binding, Methylation, Nucleotidyltransferase, Nucleus, Polymorphism, Sodium, Transferase, TRANSFERASE-DNA COMPLEX
Exp. method : X-RAY DIFFRACTION ( 2.60 Å )
Citation :

DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".

Beard, W.A.,Shock, D.D.,Batra, V.K.  et al.
(2009)  J.Biol.Chem.  284 : 31680 - 31689

PubMed: 19759017
DOI: 10.1074/jbc.M109.029843

Chain : A
UniProt : P06746 (DPOLB_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 2.7.7.7 -
-
a 5'-end 2'-deoxyribose-2'-deoxyribonucleotide-DNA = (2E,4S)- 4-hydroxypenten-2-al-5-phosphate + a 5'-end 5'-monophospho-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'-monophospho- 2'-deoxyribonucleoside-DNA + H(+) 4.2.99.18 PubMed:9614142
-