Brand  (β version)

PDB ID: 5U9H

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Ligands
Code Name Style Show Link
MN Manganese (II) ion PoSSuM
NA Sodium ion PoSSuM
PPV Pyrophosphate PoSSuM
Non-standard Residues
Code Name Show
C7R 2'-deoxy-5'-O-thiophosphonocytidine
Glycosylation
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Modification
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Structure summary

Code : 5U9H   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : DNA polymerase beta product complex with inserted Sp-isomer of dCTP-alpha-S
Release Data : 2017-02-08
Compound :
mol_id molecule chains
1 DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T
mol_id molecule chains
2 DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(C7R))-3') P
mol_id molecule chains
3 DNA (5'-D(P*GP*TP*CP*GP*G)-3') D
mol_id molecule chains
4 DNA polymerase beta A
ec: 2.7.7.7,4.2.99.-
Source :
mol_id organism_scientific
1 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific organism_common expression_system
4 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: POLB
Authors : Freudenthal, B.D., Wilson, S.H., Beard, W.A.
Keywords : transferase, lyase, DNA, TRANSFERASE-DNA complex
Exp. method : X-RAY DIFFRACTION ( 1.850 Å )
Citation :

Revealing the role of the product metal in DNA polymerase beta catalysis.

Perera, L.,Freudenthal, B.D.,Beard, W.A.  et al.
(2017)  Nucleic Acids Res.  45 : 2736 - 2745

PubMed: 28108654
DOI: 10.1093/nar/gkw1363

Reaction

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 -
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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
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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 PubMed:9614142
-